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Sample records for proton nmr coupling

  1. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224

  2. Proton zero-quantum 2D NMR of 2-propenenitrile aligned by an electric field. Determination of the 2H and 14N quadrupole coupling constants

    NASA Astrophysics Data System (ADS)

    Ruessink, B. H.; De Kanter, F. J. J.; MaClean, C.

    Zero-quantum NMR, selectively detected by 2D NMR, is applied to observe small 1H- 1H dipolar couplings in a polar liquid partially oriented by a strong electric field. The normal (single-quantum) 1H spectrum is severely broadened, which prevents the observation of small couplings. The results from the zero-quantum proton spectrum are used to calculate the 2H and 14N quadrupole coupling constants of 2-deutero-2-propenenitrile from the 2H and 14N NMR spectra.

  3. Minimalist Relativistic Force Field: Prediction of Proton-Proton Coupling Constants in (1)H NMR Spectra Is Perfected with NBO Hybridization Parameters.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-05-15

    We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz. PMID:25885091

  4. Carbon-proton scalar couplings in RNA. 3D heteronuclear and 2D isotope-edited NMR of a [sup 13]C-labeled extra-stable hairpin

    SciTech Connect

    Hines, J.V.; Landry, S.M.; Varani, G.; Tinoco, I. Jr. Lawrence Berkeley Lab., CA )

    1994-06-29

    Long range carbon-proton scalar couplings were measured for an RNA hairpin of 12 nucleotides using 3D and [sup 13]C-edited 2D NMR. The large one-bond carbon-proton scalar couplings ([sup 1]J[sub CH]) and small n-bond couplings ([sup 1]J[sub CH]) produce ECOSY type cross-peaks, thus facilitating the determination of the sign and magnitude of the smaller [sup 2]J[sub CH] or [sup 3]J[sub CH]. The UUCGRNA hairpin (5[prime]-rGGACUUCGGUCC-3[prime]), whose structure has been determined by our laboratory, was uniformly [sup 13]C-labeled at 30% isotopic enrichment. The observed [sup 1]J[sub CH] couplings were then correlated to the known structure. The signs of [sup 2]J[sub C4[prime]H5[prime

  5. Biochemical and proton NMR characterization of the isolated functional beta-subunit of coupling factor one from spinach chloroplasts

    SciTech Connect

    Roux-Fromy, M.; Neumann, J.M.; Andre, F.; Berger, G.; Girault, G.; Galmiche, J.M.; Remy, R.

    1987-04-29

    Beta subunits have been dissociated from CF1 of spinach chloroplasts, purified by HPLC and characterized by two-dimensional electrophoresis and fluorescence emission. The solutions of isolated beta subunits are able to hydrolyze MgATP; this ATPase activity is an intrinsic property of the beta molecule. From proton NMR at 300 and 500 MHz, it is shown that the preparations are fully reproducible and that beta subunits remain monomeric with 75% aliphatic protons associated with rigid parts of the molecule. The other 25% give rise to separate resonances and belong to mobile side-chains and/or to flexible regions. The measurement of the transverse relaxation times T2 has permitted a detailed characterization of the molecular dynamics of the isolated beta subunits.

  6. Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins

    NASA Astrophysics Data System (ADS)

    Linser, Rasmus; Fink, Uwe; Reif, Bernd

    2008-07-01

    Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the 15N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken α-spectrin, which was re-crystallized in H 2O/D 2O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu II to enable rapid data acquisition.

  7. Sterically Demanding Multidentate Ligand Tris[(2-(6-methylpyridyl))methyl]amine Slows Exchange and Enhances Solution State Ligand Proton NMR Coupling to 199Hg(II)

    PubMed Central

    Bebout, Deborah C.; Bush, James F.; Crahan, Kathleen K.; Bowers, Edith V.; Butcher, Raymond J.

    2006-01-01

    The solution state coordination chemistry of Hg(ClO4)2 with tris[(2-(6-methylpyridyl))methyl]amine (TLA) was investigated in acetonitrile-d3 by proton NMR. Although Hg(II) is a d10 metal ion commonly associated with notoriously rapid exchange between coordination environments, as many as six ligand environments were observed to be in slow exchange on the chemical shift time scale at select metal-to-ligand ratios. One of these ligand environments was associated with extensive heteronuclear coupling between protons and 199Hg and was assigned to the complex [Hg(TLA)]2+. The 5J(1H199Hg) = 8 Hz associated with this complex is the first example of five-bond coupling in a nitrogen coordination compound of Hg(II). The spectral complexity of related studies conducted in acetone-d6 precluded analysis of coordination equilibria. Crystallographic characterization of the T-shaped complex [Hg(TLAH)(CH2COCH3)](ClO4)2 (1) in which two pyridyl rings are pendant suggested that the acidity of acetone combined with the poor coordinating abilities of the neutral solvent adds additional complexity to solution equilibria. The complex crystallizes in the triclinic space group P1¯ with a = 9.352(2) Å, b = 12.956(2) Å, c = 14.199(2) Å, α = 115.458(10)°, β = 90.286(11)°, γ = 108.445(11)°, and Z = 2. The HgNamine, Hg-Npyridyl, and Hg-C bond lengths in the complex are 2.614(4), 2.159(4), and 2.080(6) Å, respectively. Relevance to development of 199Hg NMR as a metallobioprobe is discussed. PMID:11978122

  8. Stretched poly(methyl methacrylate) gel aligns small organic molecules in chloroform. stereochemical analysis and diastereotopic proton NMR assignment in ludartin using residual dipolar couplings and 3J coupling constant analysis.

    PubMed

    Gil, Roberto R; Gayathri, Chakicherla; Tsarevsky, Nicolay V; Matyjaszewski, Krzysztof

    2008-02-01

    Poly(methyl methacrylate) (PMMA) gels prepared by copolymerizing methyl methacrylate (MMA) and various amounts of ethylene glycol dimethacrylate (EGDMA) in the presence of the radical initiator V-70 (2,2'-azobis(2,4-dimethyl-4-methoxyvaleronitrile)) can orient small organic molecules when swollen in NMR tubes with CDCl(3). The aligning properties of the stretched PMMA gels were evaluated by monitoring the quadrupolar splitting of the (2)H NMR signal of CDCl(3), and the aligning degree is proportional to the cross-linking density. Natural abundance one-bond (1)H-(13)C residual dipolar couplings (RDCs) for menthol measured in the gels depended on the cross-link density. The stereochemistry and assignment of the diastereotopic protons of the gastroprotective and nonsteroidal aromatase inhibitor sesquiterpene lactone ludartin, isolated from Stevia yaconensis var. subeglandulosa, were unambiguously determined using a combination of natural abundance one-bond (1)H-(13)C RDCs measured in a PMMA gel and a (3)J coupling constant analysis. PMID:18177050

  9. Resolution and measurement of heteronuclear dipolar couplings of a noncrystalline protein immobilized in a biological supramolecular assembly by proton-detected MAS solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Park, Sang Ho; Yang, Chen; Opella, Stanley J.; Mueller, Leonard J.

    2013-12-01

    Two-dimensional 15N chemical shift/1H chemical shift and three-dimensional 1H-15N dipolar coupling/15N chemical shift/1H chemical shift MAS solid-state NMR correlation spectra of the filamentous bacteriophage Pf1 major coat protein show single-site resolution in noncrystalline, intact-phage preparations. The high sensitivity and resolution result from 1H detection at 600 MHz under 50 kHz magic angle spinning using ∼0.5 mg of perdeuterated and uniformly 15N-labeled protein in which the exchangeable amide sites are partially or completely back-exchanged (reprotonated). Notably, the heteronuclear 1H-15N dipolar coupling frequency dimension is shown to select among 15N resonances, which will be useful in structural studies of larger proteins where the resonances exhibit a high degree of overlap in multidimensional chemical shift correlation spectra.

  10. Proton-Coupled Electron Transfer

    SciTech Connect

    Weinberg, Dave; Gagliardi, Christopher J.; Hull, Jonathan F; Murphy, Christine Fecenko; Kent, Caleb A.; Westlake, Brittany C.; Paul, Amit; Ess, Daniel H; McCafferty, Dewey Granville; Meyer, Thomas J

    2012-07-11

    Proton-Coupled Electron Transfer (PCET) describes reactions in which there is a change in both electron and proton content between reactants and products. It originates from the influence of changes in electron content on acid-base properties and provides a molecular-level basis for energy transduction between proton transfer and electron transfer. Coupled electron-proton transfer or EPT is defined as an elementary step in which electrons and protons transfer from different orbitals on the donor to different orbitals on the acceptor. There is (usually) a clear distinction between EPT and H-atom transfer (HAT) or hydride transfer, in which the transferring electrons and proton come from the same bond. Hybrid mechanisms exist in which the elementary steps are different for the reaction partners. EPT pathways such as PhO•/PhOH exchange have much in common with HAT pathways in that electronic coupling is significant, comparable to the reorganization energy with H{sub DA} ~ λ. Multiple-Site Electron-Proton Transfer (MS-EPT) is an elementary step in which an electron-proton donor transfers electrons and protons to different acceptors, or an electron-proton acceptor accepts electrons and protons from different donors. It exploits the long-range nature of electron transfer while providing for the short-range nature of proton transfer. A variety of EPT pathways exist, creating a taxonomy based on what is transferred, e.g., 1e-/2H+ MS-EPT. PCET achieves “redox potential leveling” between sequential couples and the buildup of multiple redox equivalents, which is of importance in multielectron catalysis. There are many examples of PCET and pH-dependent redox behavior in metal complexes, in organic and biological molecules, in excited states, and on surfaces. Changes in pH can be used to induce electron transfer through films and over long distances in molecules. Changes in pH, induced by local electron transfer, create pH gradients and a driving

  11. Theoretical and experimental study of 15N NMR protonation shifts.

    PubMed

    Semenov, Valentin A; Samultsev, Dmitry O; Krivdin, Leonid B

    2015-06-01

    A combined theoretical and experimental study revealed that the nature of the upfield (shielding) protonation effect in 15N NMR originates in the change of the contribution of the sp(2)-hybridized nitrogen lone pair on protonation resulting in a marked shielding of nitrogen of about 100 ppm. On the contrary, for amine-type nitrogen, protonation of the nitrogen lone pair results in the deshielding protonation effect of about 25 ppm, so that the total deshielding protonation effect of about 10 ppm is due to the interplay of the contributions of adjacent natural bond orbitals. A versatile computational scheme for the calculation of 15N NMR chemical shifts of protonated nitrogen species and their neutral precursors is proposed at the density functional theory level taking into account solvent effects within the supermolecule solvation model. PMID:25891386

  12. Cation Hydration Constants by Proton NMR: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Smith, Robert L.; And Others

    1988-01-01

    Studies the polarization effect on water by cations and anions. Describes an experiment to illustrate the polarization effect of sodium, lithium, calcium, and strontium ions on the water molecule in the hydration spheres of the ions. Analysis is performed by proton NMR. (MVL)

  13. Synthesis and Proton NMR Spectroscopy of Intra-Vesicular Gamma-Aminobutyric Acid (GABA)*

    PubMed Central

    Wang, Luke Y.-J.; Tong, Rong; Kohane, Daniel S.

    2014-01-01

    We report the synthesis of vesicles containing gamma-aminobutyric acid (GABA), and their proton nuclear magnetic resonance (1H NMR) spectra. These vesicles were constructed to more closely mimic the intracellular environment wherein GABA exists. For this study, these GABA-containing vesicles were examined under 1H NMR as a potential platform for future studies on the differences between aqueous phantoms, ex vivo brain extracts, and in vivo magnetic resonance spectroscopy results. We found that intra-vesicular GABA faithfully yielded the chemical shifts and J-coupling constants of free aqueous GABA, alongside the chemical shift signals of the vesicle wall. PMID:24109882

  14. NMR Observation of Mobile Protons in Proton-Implanted ZnO Nanorods

    NASA Astrophysics Data System (ADS)

    Park, Jun Kue; Kwon, Hyeok-Jung; Lee, Cheol Eui

    2016-03-01

    The diffusion properties of H+ in ZnO nanorods are investigated before and after 20 MeV proton beam irradiation by using 1H nuclear magnetic resonance (NMR) spectroscopy. Herein, we unambiguously observe that the implanted protons occupy thermally unstable site of ZnO, giving rise to a narrow NMR line at 4.1 ppm. The activation barrier of the implanted protons was found to be 0.46 eV by means of the rotating-frame spin-lattice relaxation measurements, apparently being interstitial hydrogens. High-energy beam irradiation also leads to correlated jump diffusion of the surface hydroxyl group of multiple lines at ~1 ppm, implying the presence of structural disorder at the ZnO surface.

  15. NMR Observation of Mobile Protons in Proton-Implanted ZnO Nanorods

    PubMed Central

    Park, Jun Kue; Kwon, Hyeok-Jung; Lee, Cheol Eui

    2016-01-01

    The diffusion properties of H+ in ZnO nanorods are investigated before and after 20 MeV proton beam irradiation by using 1H nuclear magnetic resonance (NMR) spectroscopy. Herein, we unambiguously observe that the implanted protons occupy thermally unstable site of ZnO, giving rise to a narrow NMR line at 4.1 ppm. The activation barrier of the implanted protons was found to be 0.46 eV by means of the rotating-frame spin-lattice relaxation measurements, apparently being interstitial hydrogens. High-energy beam irradiation also leads to correlated jump diffusion of the surface hydroxyl group of multiple lines at ~1 ppm, implying the presence of structural disorder at the ZnO surface. PMID:26988733

  16. Proton conductors by the NMR method with modulation

    SciTech Connect

    Erofeev, L.N.; Sosikov, A.I.; Shteinberg, V.G.

    1988-01-01

    The NMR spectra and NMR relaxation in hydrates of phosphoro tungstic acid (PTA) and its salt were investigated. There was a narrow central line in both spectra, and the linewidth, measured in the temperature interval 130-290 K, was 4kHz. A previously proposed modulation technique by L. N. Erofeev, A.I. Sosikow, and A. K. Khitrin, was used to clarify the nature of the observed spectra. It was confirmed that model samples (gypsum, adamantane, rubber) make it possible to use the modulation technique to study the structure of proton systems. Decay curves for the magnetization in samples of PTA and Na-PTA are presented as obtained under multi-pulse spin locking conditions with and without modulation.

  17. Proton NMR studies of functionalized nanoparticles in aqueous environments

    NASA Astrophysics Data System (ADS)

    Tataurova, Yulia Nikolaevna

    in high-resolution NMR spectra. This technique is selective for protons on the surface organic functional groups due to their motional averaging in solution. In this study, 1H solution NMR spectroscopy was used to investigate the interface of the organic functional groups in D2O. The pKa for these functional groups covalently bound to the surface of nanoparticles was determined using an NMR-pH titration method based on the variation in the proton chemical shift for the alkyl group protons closest to the amine group with pH. The adsorption of toxic contaminants (chromate and arsenate anions) on the surface of functionalized silicalite-1 and mesoporous silica nanoparticles has been studied by 1H solution NMR spectroscopy. With this method, the surface bound contaminants are detected. The analysis of the intensity and position of these peaks allows quantitative assessment of the relative amounts of functional groups with adsorbed metal ions. These results demonstrate the sensitivity of solution NMR spectroscopy to the electronic environment and structure of the surface functional groups on porous nanomaterials.

  18. Heteronuclear NMR of DNA with the heteronucleus in natural abundance: facilitated assignment and extraction of coupling constants.

    PubMed Central

    Schmieder, P; Ippel, J H; van den Elst, H; van der Marel, G A; van Boom, J H; Altona, C; Kessler, H

    1992-01-01

    Two heteronuclear proton-carbon NMR experiments are applied to the DNA-octamer d(TTGGCCAA)2 with carbon in natural abundance. They lead to a complete assignment of the carbon resonances of the sugars and bases. In addition, several heteronuclear coupling constants, proton-carbon as well as proton-phosphorous and phosphorous-carbon, were determined. The information can be obtained in a reasonable measuring time and offers valuable information for a detailed picture of DNA structure. PMID:1408787

  19. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

    PubMed Central

    2016-01-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  20. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

    PubMed

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent

    2016-02-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  1. HyperBIRD: a sensitivity-enhanced approach to collecting homonuclear-decoupled proton NMR spectra.

    PubMed

    Donovan, Kevin J; Frydman, Lucio

    2015-01-01

    Samples prepared following dissolution dynamic nuclear polarization (DNP) enable the detection of NMR spectra from low-γ nuclei with outstanding sensitivity, yet have limited use for the enhancement of abundant species like (1)H nuclei. Small- and intermediate-sized molecules, however, show strong heteronuclear cross-relaxation effects: spontaneous processes with an inherent isotopic selectivity, whereby only the (13)C-bonded protons receive a polarization enhancement. These effects are here combined with a recently developed method that delivers homonuclear-decoupled (1)H spectra in natural abundance samples based on heteronuclear couplings to these same, (13)C-bonded nuclei. This results in the HyperBIRD methodology; a single-shot combination of these two effects that can simultaneously simplify and resolve complex, congested (1)H NMR spectra with many overlapping spin multiplets, while achieving 50-100 times sensitivity enhancements over conventional thermal counterparts. PMID:25256418

  2. Intermediate couplings: NMR at the solids-liquids interface

    NASA Astrophysics Data System (ADS)

    Spence, Megan

    2006-03-01

    Anisotropic interactions like dipolar couplings and chemical shift anisotropy have long offered solid-state NMR spectroscopists valuable structural information. Recently, solution-state NMR structural studies have begun to exploit residual dipolar couplings of biological molecules in weakly anisotropic solutions. These residual couplings are about 0.1% of the coupling magnitudes observed in the solid state, allowing simple, high-resolution NMR spectra to be retained. In this work, we examine the membrane-associated opioid, leucine enkephalin (lenk), in which the ordering is ten times larger than that for residual dipolar coupling experiments, requiring a combination of solution-state and solid-state NMR techniques. We adapted conventional solid-state NMR techniques like adiabatic cross- polarization and REDOR for use with such a system, and measured small amide bond dipolar couplings in order to determine the orientation of the amide bonds (and therefore the peptide) with respect to the membrane surface. However, the couplings measured indicate large structural rearrangements on the surface and contradict the published structures obtained by NOESY constraints, a reminder that such methods are of limited use in the presence of large-scale dynamics.

  3. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.

    PubMed

    Andreas, Loren B; Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Le Marchand, Tanguy; Cala-De Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido

    2016-08-16

    Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins. PMID:27489348

  4. Line-narrowing in proton-detected nitrogen-14 NMR

    NASA Astrophysics Data System (ADS)

    Cavadini, Simone; Vitzthum, Veronika; Ulzega, Simone; Abraham, Anuji; Bodenhausen, Geoffrey

    2010-01-01

    In solids spinning at the magic angle, the indirect detection of single-quantum (SQ) and double-quantum (DQ) 14N spectra ( I = 1) via spy nuclei S = 1/2 such as protons can be achieved in the manner of heteronuclear single- or multiple-quantum correlation (HSQC or HMQC) spectroscopy. The HMQC method relies on the excitation of two-spin coherences of the type T11IT11S and T21IT11S at the beginning of the evolution interval t1. The spectra obtained by Fourier transformation from t1 to ω1 may be broadened by the homogenous decay of the transverse terms of the spy nuclei S. This broadening is mostly due to homonuclear dipolar S- S' interactions between the proton spy nuclei. In this work we have investigated the possibility of inserting rotor-synchronized symmetry-based C or R sequences and decoupling schemes such as Phase-Modulated Lee-Goldburg (PMLG) sequences in the evolution period. These schemes reduce the homonuclear proton-proton interactions and lead to an enhancement of the resolution of both SQ and DQ proton-detected 14N HMQC spectra. In addition, we have investigated the combination of HSQC with symmetry-based sequences and PMLG and shown that the highest resolution in the 14N dimension is achieved by using HSQC in combination with symmetry-based sequences of the R-type. We show improvements in resolution in samples of L-alanine and the tripeptide ala-ala-gly (AAG). In particular, for L-alanine the width of the 14N SQ peak is reduced from 2 to 1.2 kHz, in agreement with simulations. We report accurate measurements of quadrupolar coupling constants and asymmetry parameters for amide 14N in AAG peptide bonds.

  5. NMR Spectra Transformed by Electron-Nuclear Coupling as Indicator of Structural Peculiarities of Magnetically Active Molecular Systems.

    PubMed

    Voronov, Vladimir K

    2016-09-01

    The peculiarities of nuclear spin relaxation in the paramagnetic systems have been analyzed taking into account the exchange processes. The analysis is based on the modified Solomon-Bloembergen equations. In this line, the conditions of detecting of the NMR signals of samples are discussed depending on resonance frequency of the NMR spectrometer and characteristic relaxation time. On this basis, (1)H NMR spectra of cobalt semiquinolate complex have been analyzed. It has been shown that the satellite signals observed in the spectrum are caused by hyperfine coupling of the tert-butyl group protons with α and β states (localized on pz orbital of the aromatic carbon) of unpaired electron spin. The relaxation process of the resonance protons is controlled by paramagnetic dipole-dipole coupling. The contact hyperfine coupling does not contribute to the paramagnetic broadening. A mechanism involving paramagnetic molecular structures, which are responsible for intramolecular exchange processes in the cobalt semiquinolate complex, is given. PMID:27513208

  6. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    SciTech Connect

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic

  7. Water Proton NMR for In Situ Detection of Insulin Aggregates.

    PubMed

    Taraban, Marc B; Truong, Huy C; Feng, Yue; Jouravleva, Elena V; Anisimov, Mikhail A; Yu, Yihua Bruce

    2015-12-01

    The need for quality control during the manufacturing and distribution of biopharmaceuticals is becoming increasingly necessary. At present, detecting drug degradation through the monitoring of active factor aggregation is accomplished through "invasive" techniques, such as size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), and so on. Unfortunately, these analytical methods require sampling the drug by opening the drug container that renders the remaining drug unusable regardless of the outcome of the test. Visual inspection, the current non-invasive quality control method is qualitative and can only detect visible particulates. Thus, it will miss sub-visible protein aggregates. In this paper, human insulin preparations were used to demonstrate that the transverse relaxation rate of water protons R2 ((1) H2 O) can serve as a sensitive and reliable indicator to detect and quantify both visible and sub-visible protein aggregates. R2 ((1) H2 O) is measured using a wide-bore low-field bench-top NMR instrument with permanent magnets. Such analysis could be carried out without opening the drug container, thus saving a drug for further use. The results suggest a novel, economical, non-destructive in situ analytical technique that allows for on-the-site quantification of protein aggregation in biopharmaceutical products. PMID:26344698

  8. Improvements in localized proton NMR spectroscopy of human brain. Water suppression, short echo times, and 1 ml resolution

    NASA Astrophysics Data System (ADS)

    Frahm, J.; Michaelis, T.; Merboldt, K. D.; Bruhn, H.; Gyngell, M. L.; Hänicke, W.

    Considerable technical improvements are reported for localized proton NMR spectroscopy using stimulated echoes. When compared to previous results, proton NMR spectra of the human brain are now obtainable (i) with in vivo water suppression factors of ⩾1000, (ii) with only minor T2 losses and negligible distortions due to J modulation at short echo times of 10-20 ms, and (iii) from volumes of interest as small as 1-8 ml within measuring times of 1-10 min. As a consequence, the detection of cerebral metabolites is greatly facilitated. This particularly applies to the assignment of those resonances (e.g., glutamate, taurine, inositols) that suffer from strong spin-spin coupling at the field strengths commonly in use for NMR in man. Studies of regional metabolite differences, tissue heterogeneity, and focal lesions in patients benefit from the increased spatial resolution and a concomitant reduction of partial volume effects. Localized proton NMR spectroscopy was performed on young healthy volunteers. Experiments were carried out on a 2.0 T whole-body MRI/MRS system using the standard headcoil for both imaging and spectroscopy.

  9. Configurationally-Coupled Protonation of Polyproline-7.

    PubMed

    Shi, Liuqing; Holliday, Alison E; Khanal, Neelam; Russell, David H; Clemmer, David E

    2015-07-15

    Structure and dynamics regulate protein function, but much less is known about how biomolecule-solvent interactions affect the structure-function relationship. Even less is known about the thermodynamics of biomolecule-solvent interactions and how such interactions influence conformational entropy. When transferred from propanol into 40:60 propanol:water under acidic conditions, a remarkably slow protonation reaction coupled with the conversion of the polyproline-I helix (PPI, having all cis-configured peptide bonds) into polyproline-II (PPII, all trans) helix is observed in this work. Kinetics and equilibrium measurements as a function of temperature allow determination of the thermochemistry and insight into how proton transfer is regulated in this system. For the proton-transfer process, PPI(+)(PrOH) + H3O(+) → PPII(2+)(PrOH/aq) + H2O, we determine ΔG = -20 ± 19 kJ·mol(-1), ΔH = -75 ± 14 kJ·mol(-1), and ΔS= -188 ± 48 J·mol(-1)·K(-1) for the overall reaction, and values of ΔG(⧧) = 91 ± 3 kJ·mol(-1), ΔH(⧧) = 84 ± 9 kJ·mol(-1), and ΔS(⧧) = -23 ± 31 J·mol(-1)·K(-1) for the transition state. For a minor process, PPI(+)(PrOH) → PPII(+)(PrOH/aq) without protonation, we determine ΔG = -9 ± 20 kJ·mol(-1), ΔH = 64 ± 14 kJ·mol(-1), and ΔS= 247 ± 50 J·mol(-1)·K(-1). This thermochemistry yields ΔG = -10 ± 29 kJ·mol(-1), ΔH = -139 ± 20 kJ·mol(-1), and ΔS= -435 ± 70 J·mol(-1)·K(-1) for PPII(+)(PrOH/aq) + H3O(+) → PPII(2+)(PrOH/aq) +H2O. The extraordinarily slow proton transfer appears to be an outcome of configurational coupling through a PPI-like transition state. PMID:26115587

  10. Proton NMR: a convenient method for determining 2-monoacylglycerol acyl migration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The acyl migration kinetics of neat (not exposed to solvent) 2-monoacylglycerol (2-MAG) to form 1-monoacylglycerol (1-MAG) was determined using proton NMR spectroscopy to monitor the B-proton integration ratios of the two species over time. 2-MAG was synthesized by the Novozym 435-catalyzed alcohol...

  11. Improving the resolution in proton-detected through-space heteronuclear multiple quantum correlation NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Shen, Ming; Trébosc, J.; Lafon, O.; Pourpoint, F.; Hu, Bingwen; Chen, Qun; Amoureux, J.-P.

    2014-08-01

    Connectivities and proximities between protons and low-gamma nuclei can be probed in solid-state NMR spectroscopy using two-dimensional (2D) proton-detected heteronuclear correlation, through Heteronuclear Multiple Quantum Correlation (HMQC) pulse sequence. The indirect detection via protons dramatically enhances the sensitivity. However, the spectra are often broadened along the indirect F1 dimension by the decay of heteronuclear multiple-quantum coherences under the strong 1H-1H dipolar couplings. This work presents a systematic comparison of the performances of various decoupling schemes during the indirect t1 evolution period of dipolar-mediated HMQC (D-HMQC) experiment. We demonstrate that 1H-1H dipolar decoupling sequences during t1, such as symmetry-based schemes, phase-modulated Lee-Goldburg (PMLG) and Decoupling Using Mind-Boggling Optimization (DUMBO), provide better resolution than continuous wave 1H irradiation. We also report that high resolution requires the preservation of 1H isotropic chemical shifts during the decoupling sequences. When observing indirectly broad spectra presenting numerous spinning sidebands, the D-HMQC sequence must be fully rotor-synchronized owing to the rotor-synchronized indirect sampling and dipolar recoupling sequence employed. In this case, we propose a solution to reduce artefact sidebands caused by the modulation of window delays before and after the decoupling application during the t1 period. Moreover, we show that 1H-1H dipolar decoupling sequence using Smooth Amplitude Modulation (SAM) minimizes the t1-noise. The performances of the various decoupling schemes are assessed via numerical simulations and compared to 2D 1H-{13C} D-HMQC experiments on [U-13C]-L-histidineṡHClṡH2O at various magnetic fields and Magic Angle spinning (MAS) frequencies. Great resolution and sensitivity enhancements resulting from decoupling during t1 period enable the detection of heteronuclear correlation between aliphatic protons and

  12. Proton NMR of Escherichia coli sulfite reductase: the unligated hemeprotein subunit.

    PubMed

    Kaufman, J; Spicer, L D; Siegel, L M

    1993-03-23

    The isolated hemeprotein subunit of sulfite reductase (SiR-HP) from Escherichia coli consists of a high spin ferric isobacteriochlorin (siroheme) coupled to a diamagnetic [4Fe-4S]2+ cluster. When supplied with an artificial electron donor, such as methyl viologen cation radical, SiR-HP can catalyze the six electron reductions of sulfite to sulfide and nitrite to ammonia. Thus, the hemeprotein subunit appears to represent the minimal protein structure required for multielectron reductase activity. Proton magnetic resonance spectra are reported for the first time on unligated SiR-HP at 300 MHz in all three redox states. The NMR spectrum of high spin ferric siroheme at pH 6.0 was obtained for the purpose of comparing its spectrum with that of oxidized SiR-HP. On the basis of line widths, T1 measurements, and 1D NOE experiments, preliminary assignments have been made for the oxidized enzyme in solution. The pH profile of oxidized SiR-HP is unusual in that a single resonance shows a 9 ppm shift over a range of only 3 pH units with an apparent pK = 6.7 +/- 0.2. Resonances arising from the beta-CH2 protons of cluster cysteines have been assigned using deuterium substitution for all redox states. One beta-CH2 resonance has been tentatively assigned to the bridging cysteine on the basis of chemical shift, T1, line width, and the presence of NOEs to protons from the siroheme ring. The observed pattern of hyperfine shifts can be used as a probe to measure the degree of coupling between siroheme and cluster in solution. The cluster iron sites of the resting (oxidized) enzyme are found to possess both positive and negative spin density which is in good agreement with Mossbauer results on frozen enzyme. The NMR spectrum of the 1-electron reduced form of SiR-HP is consistent with an intermediate spin (S = 1) siroheme. Intermediate spin Fe(II) hemes have only been previously observed in 4-coordinate model compounds. However, the amount of electron density transferred to the

  13. Proton NMR Spectra: Deceptively Simple and Deceptively Complex Examples.

    ERIC Educational Resources Information Center

    Gurst, J. E.; And Others

    1985-01-01

    Describes relatively simple nuclear magnetic resonance (NMR) experiments that demonstrate unexpected results of the deceptively simple and deceptively complex types. Background information, experimental procedures, and typical results obtained are included. (JN)

  14. Development and application of proton NMR methodology to lipoprotein analysis

    NASA Astrophysics Data System (ADS)

    Korhonen, Ari Juhani

    1998-11-01

    The present thesis describes the development of 1H NMR spectroscopy and its applications to lipoprotein analysis in vitro, utilizing biochemical prior knowledge and advanced lineshape fitting analysis in the frequency domain. A method for absolute quantification of lipoprotein lipids and proteins directly from the terminal methyl-CH3 resonance region of 1H NMR spectra of human blood plasma is described. Then the use of NMR methodology in time course studies of the oxidation process of LDL particles is presented. The function of the cholesteryl ester transfer protein (CETP) in lipoprotein mixtures was also assessed by 1H NMR, which allows for dynamic follow-up of the lipid transfer reactions between VLDL, LDL, and HDL particles. The results corroborated the suggestion that neutral lipid mass transfer among lipoproteins is not an equimolar heteroexchange. A novel method for studying lipoprotein particle fusion is also demonstrated. It is shown that the progression of proteolytically (α- chymotrypsin) induced fusion of LDL particles can be followed by 1H NMR spectroscopy and, moreover, that fusion can be distinguished from aggregation. In addition, NMR methodology was used to study the changes in HDL3 particles induced by phospholipid transfer protein (PLTP) in HDL3 + PLTP mixtures. The 1H NMR study revealed a gradual production of enlarged HDL particles, which demonstrated that PLTP-mediated remodeling of HDL involves fusion of the HDL particles. These applications demonstrated that the 1H NMR approach offers several advantages both in quantification and in time course studies of lipoprotein-lipoprotein interactions and of enzyme/lipid transfer protein function.

  15. Heteronuclear dipolar couplings, total spin coherence, and bilinear rotations in NMR spectroscopy

    SciTech Connect

    Garbow, J.R.

    1983-07-01

    In Chapter 1 a variety of different introductory topics are presented. The potential complexity of the nuclear magnetic resonsnace (NMR) spectra of molecules dissolved in liquid crystal solvents serves to motivate the development of multiple quantum (MQ) spectroscopy. The basics of MQ NMR are reviewed in Chapter 2. An experimental search procedure for the optimization of MQ pulse sequences is introduced. Chapter 3 discusses the application of MQ NMR techniques to the measurement of dipolar couplings in heteronuclear spin systems. The advantages of MQ methods in such systems are developed and experimental results for partially oriented (1-/sup 13/C) benzene are presented. Several pulse sequences are introduced which employ a two-step excitation of heteronuclear MQ coherence. A new multiple pulse method, involving the simultaneous irradiation of both rare and abundant spin species, is described. The problem of the broadening of MQ transitions due to magnetic field inhomogeneity is considered in Chapter 4. The method of total spin coherence transfer echo spectroscopy (TSCTES) is presented, with experimets on partially oriented acetaldehyde serving to demonstrate this new technique. TSCTES results in MQ spectra which are sensitive to all chemical shifts and spin-spin couplings and which are free of inhomogeneous broadening. In Chapter 5 the spectroscopy of spin systems of several protons and a /sup 13/C nucleus in the isotropic phase is discussed. The usefulness of the heteronuclear bilinear rotation as a calculational tool is illustrated. Compensated bilinear ..pi.. rotations, which are relatively insensitive to timing parameter missets, are presented. A new technique for homonuclear proton decoupling, Bilinear Rotation Decoupling, is described and its success in weakly coupled systems is demonstrated.

  16. Operando NMR spectroscopic analysis of proton transfer in heterogeneous photocatalytic reactions

    PubMed Central

    Wang, Xue Lu; Liu, Wenqing; Yu, Yan-Yan; Song, Yanhong; Fang, Wen Qi; Wei, Daxiu; Gong, Xue-Qing; Yao, Ye-Feng; Yang, Hua Gui

    2016-01-01

    Proton transfer (PT) processes in solid–liquid phases play central roles throughout chemistry, biology and materials science. Identification of PT routes deep into the realistic catalytic process is experimentally challenging, thus leaving a gap in our understanding. Here we demonstrate an approach using operando nuclear magnetic resonance (NMR) spectroscopy that allows to quantitatively describe the complex species dynamics of generated H2/HD gases and liquid intermediates in pmol resolution during photocatalytic hydrogen evolution reaction (HER). In this system, the effective protons for HER are mainly from H2O, and CH3OH evidently serves as an outstanding sacrificial agent reacting with holes, further supported by our density functional theory calculations. This results rule out controversy about the complicated proton sources for HER. The operando NMR method provides a direct molecular-level insight with the methodology offering exciting possibilities for the quantitative studies of mechanisms of proton-involved catalytic reactions in solid–liquid phases. PMID:27311326

  17. Operando NMR spectroscopic analysis of proton transfer in heterogeneous photocatalytic reactions.

    PubMed

    Wang, Xue Lu; Liu, Wenqing; Yu, Yan-Yan; Song, Yanhong; Fang, Wen Qi; Wei, Daxiu; Gong, Xue-Qing; Yao, Ye-Feng; Yang, Hua Gui

    2016-01-01

    Proton transfer (PT) processes in solid-liquid phases play central roles throughout chemistry, biology and materials science. Identification of PT routes deep into the realistic catalytic process is experimentally challenging, thus leaving a gap in our understanding. Here we demonstrate an approach using operando nuclear magnetic resonance (NMR) spectroscopy that allows to quantitatively describe the complex species dynamics of generated H2/HD gases and liquid intermediates in pmol resolution during photocatalytic hydrogen evolution reaction (HER). In this system, the effective protons for HER are mainly from H2O, and CH3OH evidently serves as an outstanding sacrificial agent reacting with holes, further supported by our density functional theory calculations. This results rule out controversy about the complicated proton sources for HER. The operando NMR method provides a direct molecular-level insight with the methodology offering exciting possibilities for the quantitative studies of mechanisms of proton-involved catalytic reactions in solid-liquid phases. PMID:27311326

  18. Amide proton exchange rates of a bound pepsin inhibitor determined by isotope-edited proton NMR experiments

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Stein, H.H.; BaMaung, N.

    1987-09-30

    From a series of isotope-edited proton NMR spectra, amide proton exchange rates were measured at 20 C, 30 C, and 40/sup 0/C for a tightly bound /sup 15/N-labeled tripeptide inhibitor of porcine pepsin (IC50 = 1.7 X 10(-) M). Markedly different NH exchange rates were observed for the three amide protons of the bound inhibitor. The P1 NH exchanged much more slowly than the P2 NH and P3 NH. These results are discussed in terms of the relative solvent accessibility in the active site and the role of the NH protons of the inhibitor for hydrogen bonding to the enzyme. In this study a useful approach is demonstrated for obtaining NH exchange rates on ligands bound to biomacromolecules, the knowledge of which could be of potential utility in the design of therapeutically useful nonpeptide enzyme inhibitors from peptide leads.

  19. Novel macrocyclic carriers for proton-coupled liquid membrane transport

    SciTech Connect

    Lamb, J.D.

    1991-06-10

    The objective of our research program is to elucidate the chemical principles which are responsible for the cation selectivity and permeability of liquid membranes containing macrocyclic carriers. Several new macrocyclic carriers were synthesized during the last three year period, including selenium-containing macrocycles, new crown-4 structures, and several new crown structures containing nitrogen based heterocycles as substituents in the principal macrocyclic ring. The cation binding properties of these macrocycles were investigated by potentiometric titration, calorimetric titration, solvent extraction, and NMR techniques. In addition, hydrophobic macrocycles were incorporated into dual hollow fiber membrane systems to investigate their membrane performance, especially in the proton-coupled transport mode. It was found that the dual hollow fiber system maintains the cation selectivity and permeability of supported liquid membranes, while enhancing membrane stability. The diffusion limited transport model was expanded to account for membrane solvent effects. Furthermore, Eu{sup 2+} transport was found to be similar to that of strontium and much higher than that of the lanthanides, in supported liquid membrane systems.

  20. Solid-state NMR analysis of membrane proteins and protein aggregates by proton detected spectroscopy

    PubMed Central

    Nieuwkoop, Andrew J.; Berthold, Deborah A.; Comellas, Gemma; Sperling, Lindsay J.; Tang, Ming; Shah, Gautam J.; Brea, Elliott J.; Lemkau, Luisel R.

    2012-01-01

    Solid-state NMR has emerged as an important tool for structural biology and chemistry, capable of solving atomic-resolution structures for proteins in membrane-bound and aggregated states. Proton detection methods have been recently realized under fast magic-angle spinning conditions, providing large sensitivity enhancements for efficient examination of uniformly labeled proteins. The first and often most challenging step of protein structure determination by NMR is the site-specific resonance assignment. Here we demonstrate resonance assignments based on high-sensitivity proton-detected three-dimensional experiments for samples of different physical states, including a fully-protonated small protein (GB1, 6 kDa), a deuterated microcrystalline protein (DsbA, 21 kDa), a membrane protein (DsbB, 20 kDa) prepared in a lipid environment, and the extended core of a fibrillar protein (α-synuclein, 14 kDa). In our implementation of these experiments, including CONH, CO(CA)NH, CANH, CA(CO)NH, CBCANH, and CBCA(CO)NH, dipolar-based polarization transfer methods have been chosen for optimal efficiency for relatively high protonation levels (full protonation or 100 % amide proton), fast magic-angle spinning conditions (40 kHz) and moderate proton decoupling power levels. Each H–N pair correlates exclusively to either intra- or inter-residue carbons, but not both, to maximize spectral resolution. Experiment time can be reduced by at least a factor of 10 by using proton detection in comparison to carbon detection. These high-sensitivity experiments are especially important for membrane proteins, which often have rather low expression yield. Proton-detection based experiments are expected to play an important role in accelerating protein structure elucidation by solid-state NMR with the improved sensitivity and resolution. PMID:22986689

  1. Selective excitation enables assignment of proton resonances and (1)H-(1)H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy.

    PubMed

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-07-21

    Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of (1)H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as (13)C or (15)N. In this method, after the initial preparation of proton magnetization and cross-polarization to (13)C nuclei, transverse magnetization of desired (13)C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific (13)C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of (1)H-(1)H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids. PMID:26203019

  2. Selective excitation enables assignment of proton resonances and 1H-1H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-07-01

    Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of 1H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as 13C or 15N. In this method, after the initial preparation of proton magnetization and cross-polarization to 13C nuclei, transverse magnetization of desired 13C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific 13C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of 1H-1H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.

  3. Selective excitation enables assignment of proton resonances and {sup 1}H-{sup 1}H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-07-21

    Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of {sup 1}H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as {sup 13}C or {sup 15}N. In this method, after the initial preparation of proton magnetization and cross-polarization to {sup 13}C nuclei, transverse magnetization of desired {sup 13}C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific {sup 13}C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of {sup 1}H-{sup 1}H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.

  4. High resolution NMR study of T{sub 1} magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide

    SciTech Connect

    Pravdivtsev, Andrey N.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L.; Vieth, Hans-Martin

    2014-10-21

    Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I–III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T{sub 1}-relaxation times at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.

  5. Interactions between Nafion resin and protonated dodecylamine modified montmorillonite: a solid state NMR study.

    PubMed

    Zhang, Limin; Xu, Jun; Hou, Guangjin; Tang, Huiru; Deng, Feng

    2007-07-01

    A series of nanocomposites have been prepared from perfluorosulfonylfluoride copolymer resin (Nafion) and layered montmorillonite (MMT) modified with protonated dodecylamine by conventional sol-gel intercalation. The structure of these nanocomposite materials have been characterized using FT-IR, elemental analysis, XRD and solid state NMR techniques, including 19F magic-angle spinning (MAS) NMR, 19F NMR relaxation time measurements, 29Si MAS, 1H MAS, 1H-13C cross-polarization magic-angle spinning (CPMAS), and 1H-13C heteronuclear correlation (HETCOR) 2D NMR. The results showed that thermal stability of Nafion was improved moderately by the addition of dodecylamine modified MMT without intercalation. FT-IR and 29Si MAS NMR results indicated that dodecylamine modification did not result in obvious changes in the MMT lattice structure. The XRD results showed that the protonated dodecylamine has been embedded and intercalated into the MMT interlayers, whereas Nafion was not. Elemental analysis results also suggested that some dodecylamine was adsorbed on the surface of MMT. 1H-13C HETCOR 2D NMR experiment clearly indicated that strong electrostatic interactions were present between the NH+3 group of dodecylamine and the fluorine-containing groups (CF3, OCF2, and SCF2) of Nafion resin. Such electrostatic interactions are probably the major contributors for the improved thermal stability of the resultant composite materials. PMID:17382953

  6. Magnetic couplings in the chemical shift of paramagnetic NMR.

    PubMed

    Vaara, Juha; Rouf, Syed Awais; Mareš, Jiří

    2015-10-13

    We apply the Kurland-McGarvey (J. Magn. Reson. 1970, 2, 286) theory for the NMR shielding of paramagnetic molecules, particularly its special case limited to the ground-state multiplet characterized by zero-field splitting (ZFS) interaction of the form S·D·S. The correct formulation for this problem was recently presented by Soncini and Van den Heuvel (J. Chem. Phys. 2013, 138, 054113). With the effective electron spin quantum number S, the theory involves 2S+1 states, of which all but one are low-lying excited states, between which magnetic couplings take place by Zeeman and hyperfine interactions. We investigate these couplings as a function of temperature, focusing on both the high- and low-temperature behaviors. As has been seen in work by others, the full treatment of magnetic couplings is crucial for a realistic description of the temperature behavior of NMR shielding up to normal measurement temperatures. At high temperatures, depending on the magnitude of ZFS, the effect of magnetic couplings diminishes, and the Zeeman and hyperfine interactions become effectively averaged in the thermally occupied states of the multiplet. At still higher temperatures, the ZFS may be omitted altogether, and the shielding properties may be evaluated using a doublet-like formula, with all the 2S+1 states becoming effectively degenerate at the limit of vanishing magnetic field. We demonstrate these features using first-principles calculations of Ni(II), Co(II), Cr(II), and Cr(III) complexes, which have ZFS of different sizes and signs. A non-monotonic inverse temperature dependence of the hyperfine shift is predicted for axially symmetric integer-spin systems with a positive D parameter of ZFS. This is due to the magnetic coupling terms that are proportional to kT at low temperatures, canceling the Curie-type 1/kT prefactor of the hyperfine shielding in this case. PMID:26574272

  7. Proton NMR study of the state of water in fibrin gels, plasma, and blood clots

    SciTech Connect

    Blinc, A.; Lahajnar, G.; Blinc, R.; Zidansek, A.; Sepe, A. )

    1990-04-01

    A proton NMR relaxation and pulsed field gradient self-diffusion study of water in fibrin gels, plasma, and blood clots has been performed with special emphasis on the effect of the sol-gel and shrinkage transitions. Deuteron NMR in fibrin gels was also studied to supplement the proton data. It is shown that a measurement of the water proton or deuteron T1/T2 ratio allows for a determination of the bound water fraction in all these systems. The change in the T1/T2 ratio at the shrinkage transition further allows for a determination of the surface fractal dimension of the gel if the change in the volume of the gel is known. The self-diffusion coefficient of water in these systems, which determines the transport properties of the gel, is found to be proportional to the free water fraction in both the nonshrunken and shrunken state.

  8. Theoretical analysis of proton relays in electrochemical proton-coupled electron transfer.

    PubMed

    Auer, Benjamin; Fernandez, Laura E; Hammes-Schiffer, Sharon

    2011-06-01

    The coupling of long-range electron transfer to proton transport over multiple sites plays a vital role in many biological and chemical processes. Recently the concerted proton-coupled electron transfer (PCET) reaction in a molecule with a hydrogen-bond relay inserted between the proton donor and acceptor sites was studied electrochemically. The standard rate constants and kinetic isotope effects (KIEs) were measured experimentally for this double proton transfer system and a related single proton transfer system. In the present paper, these systems are studied theoretically using vibronically nonadiabatic rate constant expressions for electrochemical PCET. Application of this approach to proton relays requires the calculation of multidimensional proton vibrational wave functions and the incorporation of multiple proton donor-acceptor motions. The decrease in proton donor-acceptor distances due to thermal fluctuations and the contributions from excited electron-proton vibronic states play important roles in these systems. The calculated KIEs and the ratio of the standard rate constants for the single and double proton transfer systems are in agreement with the experimental data. The calculations indicate that the standard PCET rate constant is lower for the double proton transfer system because of the smaller overlap integral between the ground state reduced and oxidized proton vibrational wave functions, resulting in greater contributions from excited electron-proton vibronic states with higher free energy barriers. The theory predicts that this rate constant may be increased by modifying the molecule in a manner that decreases the equilibrium proton donor-acceptor distances or alters the molecular thermal motions to facilitate the concurrent decrease of these distances. These insights may guide the design of more efficient catalysts for energy conversion devices. PMID:21524104

  9. Proton NMR study of spin dynamics in the magnetic organic chains M (hfac)3 NITEt (M =Eu3 +,Gd3 + )

    NASA Astrophysics Data System (ADS)

    Mariani, M.; Lascialfari, A.; Caneschi, A.; Ammannato, L.; Gatteschi, D.; Rettori, A.; Pini, M. G.; Cucci, C.; Borsa, F.

    2016-04-01

    In this work, we present a nuclear magnetic resonance (NMR) study of the spin dynamics in the rare-earth-based low-dimensional molecular magnetic chains Eu (hfac) 3NITEt and Gd (hfac) 3NITEt (in short, Eu-Et and Gd-Et). Although both samples are based on the same chemical building block, [(hfac) 3NITEt ] , their magnetic properties change dramatically when the Eu3 + ion, which is nonmagnetic at low temperatures, is substituted by the magnetic Gd3 + ion. The present proton NMR investigation shows that, down to the lowest investigated temperature (T =1.5 K for Gd-Et and T =3 K for Eu-Et), the Eu-Et chain behaves as a one-dimensional Heisenberg model with antiferromagnetic exchange coupling (J =-20 K) between s =1 /2 organic radicals, and has a T -independent exchange frequency (ωe=2.6 ×1012 rad/s). In the Gd-Et chain, in contrast, a competition arises between nearest-neighbor ferromagnetic coupling and next-nearest-neighbor antiferromagnetic coupling; moreover, two phase transitions have previously been found, in agreement with Villain's conjecture: a first transition, at T0=2.2 K, from a high temperature paramagnetic phase to a chiral spin liquid phase, and a second transition, at TN=1.9 K, to a three-dimensional helical spin solid phase. Contrary to the Eu-Et chain (whose three-dimensional ordering temperature is estimated to insurge at very low, TN≈0.3 K), critical spin dynamics effects have been measured in the Gd-Et chain on approaching TN=1.9 K: namely, a divergence of the proton nuclear spin-lattice relaxation rate 1 /T1 , which in turn produces a sudden wipe-out of the NMR signal in a very narrow (Δ T ˜0.04 K) temperature range above TN. Below TN, an inhomogeneous broadening of the NMR line indicates a complete spin freezing. At T0=2.2 K, instead, such critical effects are not observed because NMR measurements probe the two-spin correlation function, while the chiral spin liquid phase transition is associated with a divergence of the four

  10. Fluorine-19 NMR of solids with both homonuclear (multipulse) decoupling and pulsed proton decoupling

    NASA Astrophysics Data System (ADS)

    Scheler, Ulrich; Harris, Robin K.

    1996-11-01

    The application of multipulse and of combined rotation and multipulse spectroscopy (CRAMPS) to fluorine is demonstrated. The MREV-8 multipulse sequence is applied to average the homonuclear dipolar coupling between the fluorine nuclei. The heteronuclear dipolar coupling to the protons can be suppressed by irradiation with a synchronized sequence of π pulses at the proton frequency. MAS is applied to average the anisotropy of the chemical shift. Applications to a fluorinated adamantane derivative and to polyvinylidenedifluoride (PVDF) are shown.

  11. NMR studies of protonation and hydrogen bond states of internal aldimines of pyridoxal 5'-phosphate acid-base in alanine racemase, aspartate aminotransferase, and poly-L-lysine.

    PubMed

    Chan-Huot, Monique; Dos, Alexandra; Zander, Reinhard; Sharif, Shasad; Tolstoy, Peter M; Compton, Shara; Fogle, Emily; Toney, Michael D; Shenderovich, Ilya; Denisov, Gleb S; Limbach, Hans-Heinrich

    2013-12-01

    Using (15)N solid-state NMR, we have studied protonation and H-bonded states of the cofactor pyridoxal 5'-phosphate (PLP) linked as an internal aldimine in alanine racemase (AlaR), aspartate aminotransferase (AspAT), and poly-L-lysine. Protonation of the pyridine nitrogen of PLP and the coupled proton transfer from the phenolic oxygen (enolimine form) to the aldimine nitrogen (ketoenamine form) is often considered to be a prerequisite to the initial step (transimination) of the enzyme-catalyzed reaction. Indeed, using (15)N NMR and H-bond correlations in AspAT, we observe a strong aspartate-pyridine nitrogen H-bond with H located on nitrogen. After hydration, this hydrogen bond is maintained. By contrast, in the case of solid lyophilized AlaR, we find that the pyridine nitrogen is neither protonated nor hydrogen bonded to the proximal arginine side chain. However, hydration establishes a weak hydrogen bond to pyridine. To clarify how AlaR is activated, we performed (13)C and (15)N solid-state NMR experiments on isotopically labeled PLP aldimines formed by lyophilization with poly-L-lysine. In the dry solid, only the enolimine tautomer is observed. However, a fast reversible proton transfer involving the ketoenamine tautomer is observed after treatment with either gaseous water or gaseous dry HCl. Hydrolysis requires the action of both water and HCl. The formation of an external aldimine with aspartic acid at pH 9 also produces the ketoenamine form stabilized by interaction with a second aspartic acid, probably via a H-bond to the phenolic oxygen. We postulate that O-protonation is an effectual mechanism for the activation of PLP, as is N-protonation, and that enzymes that are incapable of N-protonation employ this mechanism. PMID:24147985

  12. Analysis of human muscle extracts by proton NMR

    SciTech Connect

    Venkatasubramanian, P.N.; Barany, M.; Arus, C.

    1986-03-01

    Perchloric acid extracts were prepared from pooled human muscle biopsies from patients diagnosed with scoliosis (SCOL) and cerebral palsy (CP). After neutralization with KOH and removal of perchlorate, the extracts were concentrated by freeze drying and dissolved in /sup 2/H/sub 2/O to contain 120 O.D. units at 280 nm per 0.5 ml. /sup 1/H NMR spectroscopy was performed with the 5 mm probe of a Varian XL300 instrument. Creatine, lactate, carnosine, and choline were the major resonances in the one-dimensional spectra of both extracts. With creatine as reference, 2.5-fold more lactate was found in SCOL than in CP, and a much smaller difference was also found in their carnosine content. Two-dimensional COSY comparison revealed several differences between the two extracts. Taurine, N-acetyl glutamate, glycerophosphoryl choline (or phosphoryl choline) and an unidentified spot were present only in the extract from SCOL but not in that from CP. On the other hand, aspartate, hydroxy-proline, carnitine and glycerophosphoryl ethanolamine were only present in CP but absent in SCOL. Alanine, cysteine, lysine and arginine appeared in both extracts without an apparent intensity difference.

  13. Non-destructive Ripeness Sensing by Using Proton NMR [Nuclear Magnetic Resonance

    DOE R&D Accomplishments Database

    Cho, Seong In; Krutz, G. W.; Stroshine, R. L.; Bellon, V.

    1990-01-01

    More than 80 kinds of fruits and vegetables are available in the United States. But only about 6 of them have their quality standards (Dull, 1986). In the 1990 Fresh Trends survey (Zind, 1990), consumers were asked to rate 16 characteristics important to their decision to purchase fresh produce. The four top ranking factors were ripeness/freshness, taste/flavor, appearance/condition and nutritional value. Of these surveyed, 96% rated ripeness/freshness as extremely important or very important. Therefore, the development of reliable grading or sorting techniques for fresh commodities is essential. Determination of fruit quality often involves cutting and tasting. Non-destructive quality control in fruit and vegetables is a goal of growers and distributors, as well as the food processing industry. Many nondestructive techniques have been evaluated including soft x-ray, optical transmission, near infrared radiation, and machine vision. However, there are few reports of successful non-destructive measurement of sugar content directly in fruit. Higher quality fruit could be harvested and available to consumers if a nondestructive sensor that detects ripeness level directly by measuring sugar content were available. Using proton Nuclear Magnetic Resonance (NMR) principle is the possibility. A nondestructive ripeness (or sweetness) sensor for fruit quality control can be developed with the proton NMR principle (Cho, 1989). Several feasibility studies were necessary for the ripeness sensor development. Main objectives in this paper was to investigate the feasibilities (1) to detect ripeness (or sweetness level) of raw fruit tissue with an high resolution proton NMR spectroscopy (200 MHz) and (2) to measure sugar content of intact fruit with a low resolution proton NMR spectroscopy (10 MHz).

  14. Non-destructive ripeness sensing by using proton NMR (Nuclear Magnetic Resonance)

    SciTech Connect

    Cho, Seong In; Krutz, G.W.; Stroshine, R.L. . Dept. of Agricultural Engineering); Bellon, V. , 34 - Montpellier )

    1990-01-01

    More than 80 kinds of fruits and vegetables are available in the United States. But only about 6 of them have their quality standards (Dull, 1986). In the 1990 Fresh Trends survey (Zind, 1990), consumers were asked to rate 16 characteristics important to their decision to purchase fresh produce. The four top ranking factors were ripeness/freshness, taste/flavor, appearance/condition and nutritional value. Of these surveyed, 96% rated ripeness/freshness as extremely important or very important. Therefore, the development of reliable grading or sorting techniques for fresh commodities is essential. Determination of fruit quality often involves cutting and tasting. Non-destructive quality control in fruit and vegetables is a goal of growers and distributors, as well as the food processing industry. Many nondestructive techniques have been evaluated including soft x-ray, optical transmission, near infrared radiation, and machine vision. However, there are few reports of successful non-destructive measurement of sugar content directly in fruit. Higher quality fruit could be harvested and available to consumers if a nondestructive sensor that detects ripeness level directly by measuring sugar content were available. Using proton Nuclear Magnetic Resonance (NMR) principle is the possibility. A nondestructive ripeness (or sweetness) sensor for fruit quality control can be developed with the proton NMR principle (Cho, 1989). Several feasibility studies were necessary for the ripeness sensor development. Main objectives in this paper was to investigate the feasibilities (1) to detect ripeness (or sweetness level) of raw fruit tissue with an high resolution proton NMR spectroscopy (200 MHz) and (2) to measure sugar content of intact fruit with a low resolution proton NMR spectroscopy (10 MHz). 7 refs., 4 figs.

  15. Solid-state proton multiple-quantum NMR spectroscopy with fast magic angle spinning

    NASA Astrophysics Data System (ADS)

    Geen, Helen; Titman, Jeremy J.; Gottwald, Johannes; Spiess, Hans W.

    1994-09-01

    The feasibility of multiple-quantum NMR spectroscopy with high resolution for protons in solids is explored. A new multiple-quantum excitation sequence suitable for use with fast magic angle spinning is described, and its performance is compared to that of both static and slow-spinning multiple-quantum methods. Modified sequences with scale the rate of development of the multiple-quantum coherences are also demonstrated, and two-dimensional double-quantum spectra of adamantane and polycarbonate are presented.

  16. Line Narrowing in Solid-State Proton NMR with Acquisition Delay

    NASA Astrophysics Data System (ADS)

    Fung, B. M.; Tong, Tat-Hung; Dollase, Thilo; Magnuson, Matthew L.

    Organic solids have extensive proton-proton dipolar interactions, and their 1H NMR linewidths are very large even with magic-angle spinning at moderate speeds. Recently it has been shown that substantial narrowing of the proton linewidths of organic solids can be achieved by using single-pulse excitation with acquisition delay or spin echo [S. Ding and C. A. McDowell, J. Magn. Reson. A111, 212 (1994); 115, 141 (1995); 117, 171 (1995)]. This interesting line-narrowing phenomenon has been further examined through the study of several amino acids, their deuterated analogs, and some aromatic compounds. The results confirm that narrow proton peaks are observed with long acquisition delay, and the peaks appear in the appropriate chemical-shift ranges for organic protons (0-10 ppm with respect to tetramethylsilane). However, except for some special cases, the observed peaks cannot be assigned to individual types of protons based on chemical-shift considerations only. To explore the reason for the line narrowing, the effect of acquisition delay on the 19F linewidth of CaF 2was also studied and compared with that on the 1H linewidths of organic solids. It is suggested that the broad proton peak in an organic solid is a superposition of numerous transitions. These transitions have different linewidths, and the narrow peaks in the spectrum remain observable with long acquisition delays.

  17. Proton-Coupled Electron Transfer Reactions with Photometric Bases Reveal Free Energy Relationships for Proton Transfer.

    PubMed

    Eisenhart, Thomas T; Howland, William C; Dempsey, Jillian L

    2016-08-18

    The proton-coupled electron transfer (PCET) oxidation of p-aminophenol in acetonitrile was initiated via stopped-flow rapid-mixing and spectroscopically monitored. For oxidation by ferrocenium in the presence of 7-(dimethylamino)quinoline proton acceptors, both the electron transfer and proton transfer components could be optically monitored in the visible region; the decay of the ferrocenium absorbance is readily monitored (λmax = 620 nm), and the absorbance of the 2,4-substituted 7-(dimethylamino)quinoline derivatives (λmax = 370-392 nm) red-shifts substantially (ca. 70 nm) upon protonation. Spectral analysis revealed the reaction proceeds via a stepwise electron transfer-proton transfer process, and modeling of the kinetics traces monitoring the ferrocenium and quinolinium signals provided rate constants for elementary proton and electron transfer steps. As the pKa values of the conjugate acids of the 2,4-R-7-(dimethylamino)quinoline derivatives employed were readily tuned by varying the substituents at the 2- and 4-positions of the quinoline backbone, the driving force for proton transfer was systematically varied. Proton transfer rate constants (kPT,2 = (1.5-7.5) × 10(8) M(-1) s(-1), kPT,4 = (0.55-3.0) × 10(7) M(-1) s(-1)) were found to correlate with the pKa of the conjugate acid of the proton acceptor, in agreement with anticipated free energy relationships for proton transfer processes in PCET reactions. PMID:27500804

  18. NMR resonance splitting of urea in stretched hydrogels: proton exchange and (1)H/(2)H isotopologues.

    PubMed

    Kuchel, Philip W; Naumann, Christoph; Chapman, Bogdan E; Shishmarev, Dmitry; Håkansson, Pär; Bacskay, George; Hush, Noel S

    2014-10-01

    Urea at ∼12 M in concentrated gelatin gel, that was stretched, gave (1)H and (2)H NMR spectral splitting patterns that varied in a predictable way with changes in the relative proportions of (1)H2O and (2)H2O in the medium. This required consideration of the combinatorics of the two amide groups in urea that have a total of four protonation/deuteration sites giving rise to 16 different isotopologues, if all the atoms were separately identifiable. The rate constant that characterized the exchange of the protons with water was estimated by back-transformation analysis of 2D-EXSY spectra. There was no (1)H NMR spectral evidence that the chiral gelatin medium had caused in-equivalence in the protons bonded to each amide nitrogen atom. The spectral splitting patterns in (1)H and (2)H NMR spectra were accounted for by intra-molecular scalar and dipolar interactions, and quadrupolar interactions with the electric field gradients of the gelatin matrix, respectively. PMID:25241007

  19. Intrinsic Proton NMR Studies of Mg(OH)2 and Ca(OH)2

    NASA Astrophysics Data System (ADS)

    Itoh, Yutaka; Isobe, Masahiko

    2016-09-01

    We studied the short proton free induction decay signals and the broad 1H NMR spectra of Mg(OH)2 and Ca(OH)2 powders at 77-355 K and 42 MHz using pulsed NMR techniques. Using a Gaussian-type back extrapolation procedure for the obscured data of the proton free induction decay signals, we obtained more precise values of the second moments of the Fourier-transformed broad NMR spectra than those in a previous report [Y. Itoh and M. Isobe, J. Phys. Soc. Jpn. 84, 113601 (2015)] and compared with the theoretical second moments. The decrease in the second moment could not account for the large decrease in the magnitude of the intrinsic proton spin-lattice relaxation rate 1/T1 from Mg(OH)2 to Ca(OH)2. The analysis of 1/T1 ∝ exp(-Eg/kBT) with Eg ˜ 0.01 eV points to a local hopping mechanism, and that of 1/T1 ∝ Tn with n ˜ 0.5 points to an anharmonic rattling mechanism.

  20. Relaxation of water protons in highly concentrated aqueous protein systems studied by 1H NMR spectroscopy.

    PubMed

    Szuminska, K; Gutsze, A; Kowalczyk, A

    2001-01-01

    Concentrated Aqueous Protein Systems, Proton Relaxation Times, Slow Chemical Exchange In this paper we present proton spin-lattice (T1) and spin-spin (T2) relaxation times measured vs. concentration, temperature, pulse interval (tauCPMG) as well as 1H NMR spectral measurements in a wide range of concentrations of bovine serum albumin (BSA) solutions. The anomalous relaxation behaviour of the water protons, similar to that observed in mammalian lenses, was found in the two most concentrated solutions (44% and 46%). The functional dependence of the spin-spin relaxation time vs. tauCPMG pulse interval and the values of the motional activation parameters obtained from the temperature dependencies of spin-lattice relaxation times suggest that the water molecule mobility is reduced in these systems. The slow exchange process on the T2 time scale is proposed to explain the obtained data. The proton spectral measurements support the hypothesis of a slow exchange mechanism in the highest concentrated solutions. From the analysis of the shape of the proton spectra the mean exchange times between bound and bulk water proton groups (tauex) have been estimated for the range of the highest concentrations (30%-46%). The obtained values are of the order of milliseconds assuring that the slow exchange condition is fulfilled in the most concentrated samples. PMID:11837660

  1. Proton NMR investigation of heme and surrounding proton in low-spin cyanide-ligated bacterial hemoglobin from Vitreoscilla.

    PubMed

    Xia, Y; Wu, J; Guang, S; Zhang, H; Liang, S; Shi, Y

    2000-02-01

    (1)H NMR spectra of low-spin cyanide-ligated bacterial hemoglobin from Vitreoscilla (VtHb-CN) are reported. The assignments of the(1)H NMR spectra of VtHb-CN have been made through MCOSY, NOESY, 1D TOE and SUPERWEFT experiments. Almost all resonance peaks of heme and ligated His85 are identified. The spin-lattice relaxation time T (1)'s and the variation relationships of chemical shifts of these peaks with temperature have been acquired, from which the distances between the measured protons and Fe(3+), and the diamagnetic chemical shifts have been acquired, respectively. The ionization constants of pK (a)'s of ligated His85 are determined through pH titration of chemical shift, which is 4.95 for ligated His85 C(2)H proton. The lower pK (a) is attributed to the influence of the Fe(3+) of carrying positive charge and the coordination of His85 and Fe(3+) of heme. PMID:18763116

  2. Thermodynamics of proton transport coupled ATP synthesis.

    PubMed

    Turina, Paola; Petersen, Jan; Gräber, Peter

    2016-06-01

    The thermodynamic H(+)/ATP ratio of the H(+)-ATP synthase from chloroplasts was measured in proteoliposomes after energization of the membrane by an acid base transition (Turina et al. 2003 [13], 418-422). The method is discussed, and all published data obtained with this system are combined and analyzed as a single dataset. This meta-analysis led to the following results. 1) At equilibrium, the transmembrane ΔpH is energetically equivalent to the transmembrane electric potential difference. 2) The standard free energy for ATP synthesis (reference reaction) is ΔG°ref=33.8±1.3kJ/mol. 3) The thermodynamic H(+)/ATP ratio, as obtained from the shift of the ATP synthesis equilibrium induced by changing the transmembrane ΔpH (varying either pHin or pHout) is 4.0±0.1. The structural H(+)/ATP ratio, calculated from the ratio of proton binding sites on the c-subunit-ring in F0 to the catalytic nucleotide binding sites on the β-subunits in F1, is c/β=14/3=4.7. We infer that the energy of 0.7 protons per ATP that flow through the enzyme, but do not contribute to shifting the ATP/(ADP·Pi) ratio, is used for additional processes within the enzyme, such as activation, and/or energy dissipation, due e.g. to internal uncoupling. The ratio between the thermodynamic and the structural H(+)/ATP values is 0.85, and we conclude that this value represents the efficiency of the chemiosmotic energy conversion within the chloroplast H(+)-ATP synthase. PMID:26940516

  3. Proton-detected solid-state NMR spectroscopy of fully protonated proteins at slow to moderate magic-angle spinning frequencies

    NASA Astrophysics Data System (ADS)

    Mote, Kaustubh R.; Madhu, Perunthiruthy K.

    2015-12-01

    1H -detection offers a substitute to the sensitivity-starved experiments often used to characterize biomolecular samples using magic-angle spinning solid-state NMR spectroscopy (MAS-ssNMR). To mitigate the effects of the strong 1H -1H dipolar coupled network that would otherwise severely broaden resonances, high MAS frequencies (>40 kHz) are often employed. Here, we have explored the alternative of stroboscopic 1H -detection at moderate MAS frequencies of 5-30 kHz using windowed version of supercycled-phase-modulated Lee-Goldburg homonuclear decoupling. We show that improved resolution in the 1H dimension, comparable to that obtainable at high spinning frequencies of 40-60 kHz without homonuclear decoupling, can be obtained in these experiments for fully protonated proteins. Along with detailed analysis of the performance of the method on the standard tri-peptide f-MLF, experiments on micro-crystalline GB1 and amyloid- β aggregates are used to demonstrate the applicability of these pulse-sequences to challenging biomolecular systems. With only two parameters to optimize, broadbanded performance of the homonuclear decoupling sequence, linear dependence of the chemical-shift scaling factor on resonance offset and a straightforward implementation under experimental conditions currently used for many biomolecular studies (viz. spinning frequencies and radio-frequency amplitudes), we expect these experiments to complement the current 13C -detection based methods in assignments and characterization through chemical-shift mapping.

  4. Temperature dependence of proton NMR relaxation times at earth's magnetic field

    NASA Astrophysics Data System (ADS)

    Niedbalski, Peter; Kiswandhi, Andhika; Parish, Christopher; Ferguson, Sarah; Cervantes, Eduardo; Oomen, Anisha; Krishnan, Anagha; Goyal, Aayush; Lumata, Lloyd

    The theoretical description of relaxation processes for protons, well established and experimentally verified at conventional nuclear magnetic resonance (NMR) fields, has remained untested at low fields despite significant advances in low field NMR technology. In this study, proton spin-lattice relaxation (T1) times in pure water and water doped with varying concentrations of the paramagnetic agent copper chloride have been measured from 6 to 92oC at earth's magnetic field (1700 Hz). Results show a linear increase of T1 with temperature for each of the samples studied. Increasing the concentration of the copper chloride greatly reduced T1 and reduced dependence on temperature. The consistency of the results with theory is an important confirmation of past results, while the ability of an ultra-low field NMR system to do contrast-enhanced magnetic resonance imaging (MRI) is promising for future applicability to low-cost medical imaging and chemical identification. This work is supported by US Dept of Defense Award No. W81XWH-14-1-0048 and the Robert A. Welch Foundation Grant No. AT-1877.

  5. The proton-coupled folate transporter: physiological and pharmacological roles.

    PubMed

    Zhao, Rongbao; Goldman, I David

    2013-12-01

    Recent studies have identified the proton-coupled folate transporter (PCFT) as the mechanism by which folates are absorbed across the apical brush-border membrane of the small intestine and across the basolateral membrane of the choroid plexus into the cerebrospinal fluid. Both processes are defective when there are loss-of-function mutations in this gene as occurs in the autosomal recessive disorder hereditary folate malabsorption. Because this transporter functions optimally at low pH, antifolates are being developed that are highly specific for PCFT in order to achieve selective delivery to malignant cells within the acidic environment of solid tumors. PCFT has a spectrum of affinities for folates and antifolates that narrows and increases at low pH. Residues have been identified that play a role in folate and proton binding, proton coupling, and oscillation of the carrier between its conformational states. PMID:24383099

  6. A Reinvestigation of Ramsey's Theory of NMR Coupling

    NASA Astrophysics Data System (ADS)

    Ajith Perera, S.; Bartlett, Rodney J.

    A systematic development of relativistic molecular Hamiltonians and various non-relativistic approximations are presented. Our starting point is the Dirac one-fermion Hamiltonian in the presence of an external electromagnetic field. The problems associated with generalizing [`]Dirac's one-fermion theory' smoothly to more than one fermion are discussed. The description of many-fermion systems within the framework of quantum electrodynamics (QED) will lead to Hamiltonians which do not suffer from the problems associated with the direct extension of [`]Dirac's one-fermion theory' to many-fermion system. An exhaustive discussion of the recent QED developments in the relevant area is not presented, except for cursory remarks for completeness. The non-relativistic form (NRF) of the many-electron relativistic Hamiltonian is developed as the working Hamiltonian. It is used to extract operators for the observables, which represent the response of a molecule to an external electromagnetic radiation field. In this study, our focus is mainly on the operators which eventually were used to calculate the nuclear magnetic resonance (NMR) chemical shifts and indirect nuclear spin-spin coupling constants.

  7. Evidence for a dipolar-coupled AM system in carnosine in human calf muscle from in vivo 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Bachert, Peter

    2003-10-01

    Spin systems with residual dipolar couplings such as creatine, taurine, and lactate in skeletal muscle tissue exhibit first-order spectra in in vivo 1H NMR spectroscopy at 1.5 T because the coupled protons are represented by (nearly) symmetrized eigenfunctions. The imidazole ring protons (H2, H4) of carnosine are suspected to form also a coupled system. The ring's stiffness could enable a connectivity between these anisochronous protons with the consequence of second-order spectra at low field strength. Our purpose was to study whether this deviation from the Paschen-Back condition can be used to detect the H2-H4 coupling in localized 1D 1H NMR spectra obtained at 1.5 T (64 MHz) from the human calf in a conventional whole-body scanner. As for the hydrogen hyperfine interaction, a Breit-Rabi equation was derived to describe the transition from Zeeman to Paschen-Back regime for two dipolar-coupled protons. The ratio of the measurable coupling strength ( Sk) and the difference in resonance frequencies of the coupled spins (Δ ω) induces quantum-state mixing of various degree upon definition of an appropriate eigenbase of the coupled spin system. The corresponding Clebsch-Gordan coefficients manifest in characteristic energy corrections in the Breit-Rabi formula. These additional terms were used to define an asymmetry parameter of the line positions as a function of Sk and Δ ω. The observed frequency shifts of the resonances were found to be consistent with this parameter within the accuracy achievable in in vivo NMR spectroscopy. Thus it was possible to identify the origin of satellite peaks of H2, H4 and to describe this so far not investigated type of residual dipolar coupling in vivo.

  8. Thermodynamic Study on the Protonation Reactions of Glyphosate in Aqueous Solution: Potentiometry, Calorimetry and NMR spectroscopy.

    PubMed

    Liu, Bijun; Dong, Lan; Yu, Qianhong; Li, Xingliang; Wu, Fengchang; Tan, Zhaoyi; Luo, Shunzhong

    2016-03-10

    Glyphosate [N-(phosphonomethyl)glycine] has been described as the ideal herbicide because of its unique properties. There is some conflicting information concerning the structures and conformations involved in the protonation process of glyphosate. Protonation may influence the chemical and physical properties of glyphosate, modifying its structure and the chemical processes in which it is involved. To better understand the species in solution associated with changes in pH, thermodynamic study (potentiometry, calorimetry and NMR spectroscopy) about the protonation pathway of glyphosate is performed. Experimental results confirmed that the order of successive protonation sites of totally deprotonated glyphosate is phosphonate oxygen, amino nitrogen, and finally carboxylate oxygen. This trend is in agreement with the most recent theoretical work in the literature on the subject ( J. Phys. Chem. A 2015, , 119 , 5241 - 5249 ). The result is important because it confirms that the protonated site of glyphosate in pH range 7-8, is not on the amino but on the phosphonate group instead. This corrected information can improve the understanding of the glyphosate chemical and biochemical action. PMID:26862689

  9. Correlation of the antimicrobial activity of salicylaldehydes with broadening of the NMR signal of the hydroxyl proton. Possible involvement of proton exchange processes in the antimicrobial activity.

    PubMed

    Elo, Hannu; Kuure, Matti; Pelttari, Eila

    2015-03-01

    Certain substituted salicylaldehydes are potent antibacterial and antifungal agents and some of them merit consideration as potential chemotherapeutic agents against Candida infections, but their mechanism of action has remained obscure. We report here a distinct correlation between broadening of the NMR signal of the hydroxyl proton of salicylaldehydes and their activity against several types of bacteria and fungi. When proton NMR spectra of the compounds were determined using hexadeuterodimethylsulfoxide as solvent and the height of the OH proton signal was measured, using the signal of the aldehyde proton as an internal standard, it was discovered that a prerequisite of potent antimicrobial activity is that the proton signal is either unobservable or relatively very low, i.e. that it is extremely broadened. Thus, none of the congeners whose OH proton signal was high were potent antimicrobial agents. Some congeners that gave a very low OH signal were, however, essentially inactive against the microbes, indicating that although drastic broadening of the OH signal appears to be a prerequisite, also other (so far unknown) factors are needed for high antimicrobial activity. Because broadening of the hydroxyl proton signal is related to the speed of the proton exchange process(es) involving that proton, proton exchange may be involved in the mechanism of action of the compounds. Further studies are needed to analyze the relative importance of different factors (such as electronic effects, strength of the internal hydrogen bond, co-planarity of the ring and the formyl group) that determine the rates of those processes. PMID:25621992

  10. Use of acetimidation in the NMR identification of neurophysin lysine protons

    SciTech Connect

    Sardana, V.; Breslow, E.

    1986-05-01

    Acetimidation of the two lysine residues of neurophysin (NP) results in localized changes in the proton magnetic resonance spectrum, allowing identification of lysine side-chain resonances. Neither peptide-binding nor protein self-association appeared to be significantly altered by acetimidation. Additionally, no significant effect of either peptide-binding or self-association on lysine epsilon-CH/sub 2/ protons was seen. However, dimerization-induced NMR changes in the 1.6-1.8 ppm region, associated with lysine ..beta..,..gamma..,sigma protons, were altered in the acetimidated protein. In particular, while the spectrum of the acetimidated NP monomer was almost identical to that of the native protein, a shoulder at 1.72 ppm in the native protein dimer was shifted upfield in the modified dimer. Additionally the direction of NMR shifts in the 1.6-1.8 ppm region normally associated with peptide binding to the NP dimer appeared to be reversed in the acetimidated protein. Binding-induced and dimerization-induced changes in all other regions of the spectrum were identical in the native and modified proteins. These results suggest that one or both NP lysine residues may be near the dimer subunit interface and indicate an effect of peptide-binding on lysine side-chain environment.

  11. Conformation analysis of d-glucaric acid in deuterium oxide by NMR based on its JHH and JCH coupling constants.

    PubMed

    Enomoto-Rogers, Yukiko; Masaki, Hisaharu; Ito, Tetsuya; Furihata, Kazuo; Iwata, Tadahisa

    2016-07-01

    d-Glucaric acid (GA) is an aldaric acid and consists of an asymmetric acyclic sugar backbone with a carboxyl group positioned at either end of its structure (i.e., the C1 and C6 positions). The purpose of this study was to conduct a conformation analysis of flexible GA as a solution in deuterium oxide by NMR spectroscopy, based on J-resolved conformation analysis using proton-proton ((3) JHH ) and proton-carbon ((2) JCH and (3) JCH ) coupling constants, as well as nuclear overhauser effect spectroscopy (NOESY). The (2) JCH and (3) JCH coupling constants were measured using the J-resolved heteronuclear multiple bond correlation (HMBC) NMR technique. NOESY correlation experiments indicated that H2 and H5 were in close proximity, despite the fact that these protons were separated by too large distance in the fully extended form of the chain structure to provide a NOESY correlation. The validities of the three possible conformers along the three different bonds (i.e., C2C3, C3C4, and C4C5) were evaluated sequentially based on the J-coupling values and the NOESY correlations. The results of these analyses suggested that there were three dominant conformers of GA, including conformer 1, which was H2H3:gauche, H3H4:anti, and H4H5:gauche; conformer 2, which was H2H3:gauche, H3H4:anti, and H4H5:anti; and conformer 3, which was H2H3:gauche, H3H4: gauche, and H4H5:anti. These results also suggested that all three of these conformers exist in equilibrium with each other. Lastly, the results of the current study suggested that the conformational structures of GA in solution were 'bent' rather than being fully extended. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26749401

  12. Uncertainty measurement for automated macro program-processed quantitative proton NMR spectra.

    PubMed

    Hays, Patrick A; Schoenberger, Torsten

    2014-11-01

    The evaluation of a fully automated quantitative proton nuclear magnetic resonance spectroscopy (qNMR) processing program, including the determination of its processing uncertainty, and the calculations of the combined uncertainty of the qNMR result, is presented with details on the use of a trimmed purity average. Quantitative NMR spectra (1359) were collected over a 4-month period on various concentrations of pseudoephedrine HCl dissolved in D2O (0.0610 to 93.60 mg/mL) containing maleic acid (the internal standard) to yield signal-to-noise ratios ranging from 3 to 72,000 for analyte integral regions. The resulting 5436 purities exhibited a normal distribution about the best estimate of the true value. The median absolute deviation (MAD) statistical method was used to obtain a model of uncertainty relative to the signal-to-noise of the analyte's integral peaks. The model was then tested using different concentrations of known purity chloroquine diphosphate. qNMR results of numerous illicit heroin HCl samples were compared to those obtained by capillary electrophoresis. PMID:25273593

  13. Protein structure determination by combining sparse NMR data with evolutionary couplings

    PubMed Central

    Tang, Yuefeng; Huang, Yuanpeng Janet; Hopf, Thomas A.; Sander, Chris; Marks, Debora S.; Montelione, Gaetano T.

    2015-01-01

    Accurate protein structure determination by NMR is challenging for larger proteins, for which experimental data is often incomplete and ambiguous. Fortunately, the upsurge in evolutionary sequence information and advances in maximum entropy statistical methods now provide a rich complementary source of structural constraints. We have developed a hybrid approach (EC-NMR) combining sparse NMR data with evolutionary residue-residue couplings, and demonstrate accurate structure determination for several 6 to 41 kDa proteins. PMID:26121406

  14. Measurement and assignment of long-range C-H dipolar couplings in liquid crystals by two-dimensional NMR spectroscopy

    SciTech Connect

    Hong, M.; Pines, A. |; Caldarelli, S.

    1996-08-29

    We describe multidimensional NMR techniques to measure and assign {sup 13}C-{sup 1}H dipolar couplings in nematic liquid crystals with high resolution. In particular, dipolar couplings between aromatic and aliphatic sites are extracted, providing valuable information on the structural correlations between these two components of thermotropic liquid crystal molecules. The NMR techniques are demonstrated on 4-pentyl-4`-biphenylcarbonitrile (5CB), a well-characterized room-temperature nematic liquid crystal. Proton-detected local-field NMR spectroscopy is employed to obtain highly resolved C-H dipolar couplings that are separated according to the chemical shifts of the carbon sites. Each {sup 13}C cross section in the 2D spectra exhibits several doublet splittings, with the largest one resulting from the directly bonded C-H coupling. The smaller splittings originate from the long-range C-H dipolar couplings and can be assigned qualitatively by a chemical shift heteronuclear correlation (HETCOR) experiment. The HETCOR experiment incorporates a mixing period for proton spin diffusion to occur, so that maximal polarization transfer can be achieved between the unbonded {sup 13}C and {sup 1}H nuclei. To assign the long-range C-H couplings quantitatively. we combined these two techniques into a novel reduced-3D experiment, in which the {sup 1}H chemical shift-displaced C-H dipolar couplings are correlated with the {sup 13}C chemical shifts. 34 refs., 6 figs., 2 tabs.

  15. Proton-coupled electron transfer in solution, proteins, and electrochemistry.

    PubMed

    Hammes-Schiffer, Sharon; Soudackov, Alexander V

    2008-11-13

    Recent advances in the theoretical treatment of proton-coupled electron transfer (PCET) reactions are reviewed. These reactions play an important role in a wide range of biological processes, as well as in fuel cells, solar cells, chemical sensors, and electrochemical devices. A unified theoretical framework has been developed to describe both sequential and concerted PCET, as well as hydrogen atom transfer (HAT). A quantitative diagnostic has been proposed to differentiate between HAT and PCET in terms of the degree of electronic nonadiabaticity, where HAT corresponds to electronically adiabatic proton transfer and PCET corresponds to electronically nonadiabatic proton transfer. In both cases, the overall reaction is typically vibronically nonadiabatic. A series of rate constant expressions have been derived in various limits by describing the PCET reactions in terms of nonadiabatic transitions between electron-proton vibronic states. These expressions account for the solvent response to both electron and proton transfer and the effects of the proton donor-acceptor vibrational motion. The solvent and protein environment can be represented by a dielectric continuum or described with explicit molecular dynamics. These theoretical treatments have been applied to numerous PCET reactions in solution and proteins. Expressions for heterogeneous rate constants and current densities for electrochemical PCET have also been derived and applied to model systems. PMID:18842015

  16. Proton and nitrogen-15 NMR spectroscopic studies of hydrogen ion-dependent pseudo-halide ion binding to chloroperoxidase

    SciTech Connect

    Lukat, G.S.; Goff, H.M.

    1986-12-15

    The proton nuclear magnetic resonance spectra of several chloroperoxidase-inhibitor complexes have been investigated. Titrations of chloroperoxidase with azide, thiocyanate, cyanate, or nitrite ions indicate that only the chloroperoxidase-thiocyanate complex exhibits slow ligand exchange on the 360-MHz NMR time scale. The temperature dependence of the proton NMR spectra of the complexes suggests that, although the complexes are predominantly low-spin ferric heme iron, a spin equilibrium is present presumably between S = 1/2 and S = 5/2 states. The pH dependence of the proton NMR spectra of the psuedo-halide-chloroperoxidase complexes was examined at 360 and 90 MHz. Chloroperoxidase complexes with azide and cyanate show similar behavior; 360-MHz proton spectra are readily observed at low pH (less than 5.0) but not at high pH. At high pH, the ligand exchange rate falls in an intermediate time range. When the complexes are examined at 90 MHz, however, spectra consisting of averaged signals are observed. The chloroperoxidase-thiocyanate complex does not form at high pH values; the proton NMR spectrum observed is that of native chloroperoxidase. The pKa for the chloroperoxidase-thiocyanate heme-linked ionizable amino acid residue falls between 4.2 and 5.0. Only an averaged azide signal was observed in the nitrogen-15 NMR spectra for solutions that contained the azide complex of chloroperoxidase, horseradish peroxidase, and myoglobin.

  17. Proton and nitrogen-15 NMR spectroscopic studies of hydrogen ion-dependent pseudo-halide ion binding to chloroperoxidase.

    PubMed

    Lukat, G S; Goff, H M

    1986-12-15

    The proton nuclear magnetic resonance spectra of several chloroperoxidase-inhibitor complexes have been investigated. Titrations of chloroperoxidase with azide, thiocyanate, cyanate, or nitrite ions indicate that only the chloroperoxidase-thiocyanate complex exhibits slow ligand exchange on the 360-MHz NMR time scale. The temperature dependence of the proton NMR spectra of the complexes suggests that, although the complexes are predominantly low-spin ferric heme iron, a spin equilibrium is present presumably between S = 1/2 and S = 5/2 states. The pH dependence of the proton NMR spectra of the psuedo-halide-chloroperoxidase complexes was examined at 360 and 90 MHz. Chloroperoxidase complexes with azide and cyanate show similar behavior; 360-MHz proton spectra are readily observed at low pH (less than 5.0) but not at high pH. At high pH, the ligand exchange rate falls in an intermediate time range. When the complexes are examined at 90 MHz, however, spectra consisting of averaged signals are observed. The chloroperoxidase-thiocyanate complex does not form at high pH values; the proton NMR spectrum observed is that of native chloroperoxidase. The pKa for the chloroperoxidase-thiocyanate heme-linked ionizable amino acid residue falls between 4.2 and 5.0. Only an averaged azide signal was observed in the nitrogen-15 NMR spectra for solutions that contained the azide complex of chloroperoxidase, horseradish peroxidase, and myoglobin. PMID:3023353

  18. Exchangers man the pumps: Functional interplay between proton pumps and proton-coupled Ca(2+) exchangers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tonoplast-localised proton-coupled Ca(2+) transporters encoded by cation/H(+) exchanger (CAX) genes play a critical role in sequestering Ca(2+) into the vacuole. These transporters may function in coordination with Ca(2+) release channels, to shape stimulus-induced cytosolic Ca(2+) elevations. Recen...

  19. Residual methyl protonation in perdeuterated proteins for multi-dimensional correlation experiments in MAS solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Agarwal, Vipin; Reif, Bernd

    2008-09-01

    NMR studies involving perdeuterated proteins focus in general on exchangeable amide protons. However, non-exchangeable sites contain as well a small amount of protons as the employed precursors for protein biosynthesis are not completely proton depleted. The degree of methyl group protonation is in the order of 9% for CD 2H using >97% deuterium enriched glucose. We show in this manuscript that this small amount of residual protonation is sufficient to perform 2D and 3D MAS solid-state NMR experiments. In particular, we suggest a HCCH-TOBSY type experiment which we successfully employ to assign the methyl resonances in aliphatic side chains in a perdeuterated sample of the SH3 domain of chicken α-spectrin.

  20. 1H NMR studies of maltose, maltoheptaose, alpha-, beta-, and gamma-cyclodextrins, and complexes in aqueous solutions with hydroxy protons as structural probes.

    PubMed

    Bekiroglu, Somer; Kenne, Lennart; Sandström, Corine

    2003-03-01

    The (1)H NMR chemical shifts, coupling constants, temperature coefficients, and exchange rates have been measured for the hydroxy protons of aqueous solutions of alpha-, beta-, and gamma-cyclodextrins, maltose, and maltoheptaose. In cyclodextrins (CDs), the high chemical shift of the O(3)H signal and its small (3)J(OH,CH) value suggest that O(3)H is involved in a hydrogen bond. The small temperature coefficients and rate of exchange values of O(2)H and O(3)H confirm the involvement of O(3)H in hydrogen bonding and indicate that O(2)H is the hydrogen bond partner. In maltose, two distinct NMR signals with two different vicinal coupling constants are found for O(2')H. A cross-peak in the ROESY spectrum indicates chemical exchange between the O(2')H and O(3)H protons. The existence of two distinct NMR signals with different J values for O(2')H shows the influence of anomeric configuration on the O(2')H-O(3)H interaction. The effect of complexation with methyl benzoate, adamantane-1-carboxylic acid, adamantane-1-ol, and l- and d-tryptophane on the NMR spectra of the hydroxy protons of alpha-, beta-, and gamma-cyclodextrins and of maltose has been investigated. No significant spectral changes were observed upon addition of methyl benzoate and adamantane-1-carboxylic acid. The addition of adamantane-1-ol resulted in an upfield shift and a strong broadening of the O(2)H signal from alpha-CD, and a small temperature coefficient was measured upon complexation. The O(2)H and O(3)H signals in beta-CD were broadened and shifted downfield upon addition of l- and d-tryptophane. PMID:12608778

  1. Symmetrization of cationic hydrogen bridges of protonated sponges induced by solvent and counteranion interactions as revealed by NMR spectroscopy.

    PubMed

    Pietrzak, Mariusz; Wehling, Jens P; Kong, Shushu; Tolstoy, Peter M; Shenderovich, Ilya G; López, Concepción; Claramunt, Rosa María; Elguero, José; Denisov, Gleb S; Limbach, Hans-Heinrich

    2010-02-01

    The properties of the intramolecular hydrogen bonds of doubly (15)N-labeled protonated sponges of the 1,8-bis(dimethylamino)naphthalene (DMANH(+)) type have been studied as a function of the solvent, counteranion, and temperature using low-temperature NMR spectroscopy. Information about the hydrogen-bond symmetries was obtained by the analysis of the chemical shifts delta(H) and delta(N) and the scalar coupling constants J(N,N), J(N,H), J(H,N) of the (15)NH(15)N hydrogen bonds. Whereas the individual couplings J(N,H) and J(H,N) were averaged by a fast intramolecular proton tautomerism between two forms, it is shown that the sum |J(N,H)+J(H,N)| generally represents a measure of the hydrogen-bond strength in a similar way to delta(H) and J(N,N). The NMR spectroscopic parameters of DMANH(+) and of 4-nitro-DMANH(+) are independent of the anion in the case of CD(3)CN, which indicates ion-pair dissociation in this solvent. By contrast, studies using CD(2)Cl(2), [D(8)]toluene as well as the freon mixture CDF(3)/CDF(2)Cl, which is liquid down to 100 K, revealed an influence of temperature and of the counteranions. Whereas a small counteranion such as trifluoroacetate perturbed the hydrogen bond, the large noncoordinating anion tetrakis[3,5-bis(trifluoromethyl)phenyl]borate B[{C(6)H(3)(CF(3))(2)}(4)](-) (BARF(-)), which exhibits a delocalized charge, made the hydrogen bond more symmetric. Lowering the temperature led to a similar symmetrization, an effect that is discussed in terms of solvent ordering at low temperature and differential solvent order/disorder at high temperatures. By contrast, toluene molecules that are ordered around the cation led to typical high-field shifts of the hydrogen-bonded proton as well as of those bound to carbon, an effect that is absent in the case of neutral NHN chelates. PMID:20024986

  2. Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters

    PubMed Central

    Morris, Wesley D.; Darcy, Julia W.; Mayer, James M.

    2015-01-01

    Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4S4(SAr)4]2- (1, SAr = S-2,4-6-(iPr)3C6H2) leads to thiol dissociation, reversibly forming [Fe4S4(SAr)3L]1- (2) + ArSH (L = solvent, and/or conjugate base). Solutions of 2 + ArSH react with the nitroxyl radical TEMPO to give [Fe4S4(SAr)4]1- (1ox) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4S4(SAr)3(HSAr)]1-(1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

  3. Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters.

    PubMed

    Saouma, Caroline T; Morris, Wesley D; Darcy, Julia W; Mayer, James M

    2015-06-15

    Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4 S4 (SAr)4 ](2-) (1, SAr=S-2,4-6-(iPr)3 C6 H2 ) leads to thiol dissociation, reversibly forming [Fe4 S4 (SAr)3 L](1-) (2) and ArSH (L=solvent, and/or conjugate base). Solutions of 2+ArSH react with the nitroxyl radical TEMPO to give [Fe4 S4 (SAr)4 ](1-) (1ox ) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4 S4 (SAr)3 (HSAr)](1-) (1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

  4. ¹H and (15)N NMR Analyses on Heparin, Heparan Sulfates and Related Monosaccharides Concerning the Chemical Exchange Regime of the N-Sulfo-Glucosamine Sulfamate Proton.

    PubMed

    Pomin, Vitor H

    2016-01-01

    Heparin and heparan sulfate are structurally related glycosaminoglycans (GAGs). Both GAGs present, although in different concentrations, N-sulfo-glucosamine (GlcNS) as one of their various composing units. The conditional fast exchange property of the GlcNS sulfamate proton in these GAGs has been pointed as the main barrier to its signal detection via NMR experiments, especially ¹H-(15)N HSQC. Here, a series of NMR spectra is collected on heparin, heparan sulfate and related monosaccharides. The N-acetyl glucosamine-linked uronic acid types of these GAGs were properly assigned in the ¹H-(15)N HSQC spectra. Dynamic nuclear polarization (DNP) was employed in order to facilitate 1D spectral acquisition of the sulfamate (15)N signal of free GlcNS. Analyses on the multiplet pattern of scalar couplings of GlcNS (15)N has helped to understand the chemical properties of the sulfamate proton in solution. The singlet peak observed for GlcNS happens due to fast chemical exchange of the GlcNS sulfamate proton in solution. Analyses on kinetics of alpha-beta anomeric mutarotation via ¹H NMR spectra have been performed in GlcNS as well as other glucose-based monosaccharides. 1D ¹H and 2D ¹H-(15)N HSQC spectra recorded at low temperature for free GlcNS dissolved in a proton-rich solution showed signals from all exchangeable protons, including those belonging to the sulfamate group. This work suits well to the current grand celebration of one-century-anniversary of the discovery of heparin. PMID:27618066

  5. Low Temperature 1H MAS NMR Spectroscopy Studies of Proton Motion in Zeolite

    SciTech Connect

    Huo, H.; Peng, L; Grey, C

    2009-01-01

    Low temperature {sup 1}H MAS NMR spectroscopy is used to study protonic motion in zeolite HZSM-5 in both samples that have been dried using procedures that are standard in the literature and samples that have been more carefully dehydrated. A significant enhancement of proton mobility is seen for the ''standard'' dehydrated HZSM-5 sample in comparison to that seen for the much drier sample. This is ascribed to a vehicle-hopping mechanism involving the residual water that is present in these zeolites. A gradual change of the framework structure is observed on cooling to approximately 213 K, as monitored via the change in {sup 1}H chemical shift values of the Broensted acid resonances and by X-ray diffraction. A more sudden change in structure is seen by differential scanning calorimetry and NMR at approximately 220?230 K, which is associated with changes in both the mobility and the modes of binding of the residual water to the Broensted acid sites and the zeolite framework.

  6. 1H NMR study of proton dynamics in the inorganic solid acid Rb3 H( SO4 )2

    NASA Astrophysics Data System (ADS)

    Suzuki, Koh-Ichi; Hayashi, Shigenobu

    2006-01-01

    Proton dynamics in Rb3H(SO4)2 has been studied by means of H1 NMR. The H1 magic-angle-spinning (MAS) NMR spectra were traced at room temperature (RT) at Larmor frequency of 400.13MHz . H1 static NMR spectra were measured at frequencies of 200.13MHz and 400.13MHz in the ranges of 165-513 and 300-513K , respectively. H1 spin-lattice relaxation times, T1 , were measured at 200.13 and 19.65MHz in the ranges of 260-513 and 260-470K , respectively. The H1 MAS NMR spectrum at 294K has an isotropic chemical shift of 16.3ppm from tetramethylsilane, demonstrating very strong hydrogen bonds. In RT phase, a wobbling motion of the O-H axis in one direction at the fast motional limit takes place above 400K , being supported by the H1 static NMR spectral line shapes and by the H1 T1 values. In the high temperature (HT) phase, the sharp H1 static NMR spectra indicate translational proton diffusion. From the analysis of H1 T1 , protons diffuse with the inverse of the frequency factor (τ0) of 9.5×10-13s and the activation energy (Ea) of 25kJmol-1 . These parameters can well explain the macroscopic electric conductivity in HT phase.

  7. Nanoantioxidant-driven plasmon enhanced proton-coupled electron transfer

    NASA Astrophysics Data System (ADS)

    Sotiriou, Georgios A.; Blattmann, Christoph O.; Deligiannakis, Yiannis

    2015-12-01

    Proton-coupled electron transfer (PCET) reactions involve the transfer of a proton and an electron and play an important role in a number of chemical and biological processes. Here, we describe a novel phenomenon, plasmon-enhanced PCET, which is manifested using SiO2-coated Ag nanoparticles functionalized with gallic acid (GA), a natural antioxidant molecule that can perform PCET. These GA-functionalized nanoparticles show enhanced plasmonic response at near-IR wavelengths, due to particle agglomeration caused by the GA molecules. Near-IR laser irradiation induces strong local hot-spots on the SiO2-coated Ag nanoparticles, as evidenced by surface enhanced Raman scattering (SERS). This leads to plasmon energy transfer to the grafted GA molecules that lowers the GA-OH bond dissociation enthalpy by at least 2 kcal mol-1 and therefore facilitates PCET. The nanoparticle-driven plasmon-enhancement of PCET brings together the so far unrelated research domains of nanoplasmonics and electron/proton translocation with significant impact on applications based on interfacial electron/proton transfer.Proton-coupled electron transfer (PCET) reactions involve the transfer of a proton and an electron and play an important role in a number of chemical and biological processes. Here, we describe a novel phenomenon, plasmon-enhanced PCET, which is manifested using SiO2-coated Ag nanoparticles functionalized with gallic acid (GA), a natural antioxidant molecule that can perform PCET. These GA-functionalized nanoparticles show enhanced plasmonic response at near-IR wavelengths, due to particle agglomeration caused by the GA molecules. Near-IR laser irradiation induces strong local hot-spots on the SiO2-coated Ag nanoparticles, as evidenced by surface enhanced Raman scattering (SERS). This leads to plasmon energy transfer to the grafted GA molecules that lowers the GA-OH bond dissociation enthalpy by at least 2 kcal mol-1 and therefore facilitates PCET. The nanoparticle-driven plasmon

  8. Transverse beam coupling impedance of the CERN Proton Synchrotron

    NASA Astrophysics Data System (ADS)

    Persichelli, S.; Migliorati, M.; Biancacci, N.; Gilardoni, S.; Metral, E.; Salvant, B.

    2016-04-01

    Beam coupling impedance is a fundamental parameter to characterize the electromagnetic interaction of a particle beam with the surrounding environment. Synchrotron machine performances are critically affected by instabilities and collective effects triggered by beam coupling impedance. In particular, transverse beam coupling impedance is expected to impact beam dynamics of the CERN Proton Synchrotron (PS), since a significant increase in beam intensity is foreseen within the framework of the LHC Injectors Upgrade (LIU) project. In this paper we describe the study of the transverse beam coupling impedance of the PS, taking into account the main sources of geometrical impedance and the contribution of indirect space charge at different energies. The total machine impedance budget, determined from beam-based dedicated machine measurement sessions, is also discussed and compared with the theoretical model.

  9. Surface NMR measurement of proton relaxation times in medium to coarse-grained sand aquifer.

    PubMed

    Shushakov, O A

    1996-01-01

    A surface NMR investigation of groundwater in the geomagnetic field is under study. To detect the surface NMR a wire loop with a diameter of about 100 m, being an antenna for both an exciting field source and the NMR signal receiver, is laid out on the ground. A sinusoidal current pulse with a rectangular envelope is passed through the loop to excite the NMR signal. The carrier frequency of the oscillating current in this pulse is equal to the Larmor frequency of protons in the Earth's magnetic field. The current amplitude is changed up to 200 amps and the pulse duration is fixed and is equal to 40 ms. The exciting pulse is followed by an induction emf signal caused by the Larmor nuclear precession in geomagnetic field. The relaxation times T1, T2, and T2* were measured by the surface NMR for both groundwater in medium to coarse-grained sand at borehole and for bulk water under the ice surface of frozen lake. To determine T1, a longitudinal interference in experiments with repeated pulses was measured. A sequence with equal period between equal excitation pulses was used. The relaxation times T1, T2, measured for bulk water under the ice of the Ob reservoir were 1.0 s and 0.7 s, respectively. To estimate an influence of dissolved oxygen T1 of the same water at the same temperature was measured by lab NMR with and without pumping of oxygen. The relaxation time T1 measured for water in the medium to coarse-grained sand is 0.65 s. The relaxation time T2 estimated by spin echo sequence is found to be equal to 0.15 s. The relaxation time T2* is found to be about 80 ms. This result contradicts published earlier phenomenological correlation between relaxation time T2* and grain size of water-bearing rock. This could be as a result of unsound approach based on grain size or influence of paramagnetic impurities. PMID:8970122

  10. Integrating proton coupled electron transfer (PCET) and excited states

    SciTech Connect

    Gagliardi, Christopher J.; Westlake, Brittany C.; Kent, Caleb A.; Paul, Jared J.; Papanikolas, John M.; Meyer, Thomas J.

    2010-11-01

    In many of the chemical steps in photosynthesis and artificial photosynthesis, proton coupled electron transfer (PCET) plays an essential role. An important issue is how excited state reactivity can be integrated with PCET to carry out solar fuel reactions such as water splitting into hydrogen and oxygen or water reduction of CO2 to methanol or hydrocarbons. The principles behind PCET and concerted electron–proton transfer (EPT) pathways are reasonably well understood. In Photosystem II antenna light absorption is followed by sensitization of chlorophyll P680 and electron transfer quenching to give P680+. The oxidized chlorophyll activates the oxygen evolving complex (OEC), a CaMn4 cluster, through an intervening tyrosine–histidine pair, YZ. EPT plays a major role in a series of four activation steps that ultimately result in loss of 4e-/4H+ from the OEC with oxygen evolution. The key elements in photosynthesis and artificial photosynthesis – light absorption, excited state energy and electron transfer, electron transfer activation of multiple-electron, multiple-proton catalysis – can also be assembled in dye sensitized photoelectrochemical synthesis cells (DS-PEC). In this approach, molecular or nanoscale assemblies are incorporated at separate electrodes for coupled, light driven oxidation and reduction. Separate excited state electron transfer followed by proton transfer can be combined in single semi-concerted steps (photo-EPT) by photolysis of organic charge transfer excited states with H-bonded bases or in metal-to-ligand charge transfer (MLCT) excited states in pre-associated assemblies with H-bonded electron transfer donors or acceptors. In these assemblies, photochemically induced electron and proton transfer occur in a single, semi-concerted event to give high-energy, redox active intermediates.

  11. Analysis of the carbon-13 and proton NMR spectra of bovine chromaffin granules.

    PubMed

    Sharp, R R; Richards, E P

    1977-03-29

    Natural abundance carbon-13 and proton NMR spectra of bovine chromaffin granules have been obtained and analyzed using computer simulation techniques. High resolution spectra show the presence of a fluid aqueous phase containing epinephrine, ATP and a random coil protein. The protein spectrum contains unusually intense resonances due to glutamic acid and proline and has been simulated satisfactorily using the known amino acid composition of chromogranin A. The lipid phase of chromaffin granules gives rise to intense, but very broad, resonances in the carbon-13 spectrum. Protons in the lipid phase are also observable as a very rapid component of the proton-free induction decay (T2 approximately equal to 15 microns). Linewidths of the carbon-13 spectra have been used to set upper limits on rotational correlation times and on the motional anisotropy in the aqueous phase. These limits show that the aqueous phase is a simple solution (not a gel) that is isotropic over regions much larger than solute dimensions. No gel transition is observed between -3 and 25 degrees C. The carbon-13 spectra are definitely inconsistent with a lipoprotein matrix model and chromaffin granules previously proposed by Helle and Serck-Hanssen ((1975) Mol. Cell, Biochem. 6, 127-146). Relative carbon-13 intensities of ATP and epinephrine are not consistent with the known 1 : 4 mol ratio of these components. This fact suggests that epinephrine and ATP are not directly complexed in intact chromaffin granules. PMID:849474

  12. Proton-detected 2D radio frequency driven recoupling solid-state NMR studies on micelle-associated cytochrome-b5

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2014-05-01

    Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.

  13. Proton-Detected 2D Radio Frequency Driven Recoupling Solid-state NMR Studies on Micelle-associated Cytochrome-b5

    PubMed Central

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2014-01-01

    Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles. PMID:24657390

  14. New approach for characterization of gelatin biopolymer films using proton behavior determined by low field 1H NMR spectrometry.

    PubMed

    Kim, Young-Teck; Hong, Young-Shick; Kimmel, Robert M; Rho, Jeong-Hae; Lee, Cherl-Ho

    2007-12-26

    The behavior of protons in biopolymer films (BFs) formed with gelatin, water, and glycerol was investigated at various relative humidities (RHs) and concentrations of glycerol using a low field 1H NMR spectrometer. At a RH of approximately 0%, the distributed spin-spin relaxation times (T2) of protons in BFs showed two components: a rapidly relaxing proton with the shortest T2 derived from protons in the rigid backbone of the gelatin polymer such as CH1-, CH2-, and CH3-, and a slowly relaxing component with longer T2 from protons of the functional groups in amino acid residues in gelatin such as -OH, -COOH, and -NH3. These two components are referred to as nonexchangeable (T2N) and exchangeable protons (T2E), respectively, indicating the different mobility of the protons. The T2E increased as RH increased indicating the increase in relative mobility of protons due to the larger free volume in the BF matrix. Above a RH of 33%, the slowest relaxing component was found in all BFs and referred to as hydration-water protons (T2W) with the highest relative mobility of all protons in the films. It suggests that the free volume in BFs can be formed above a RH of 33% in the absence of glycerol. The behaviors of T2N, T2E, and T2W reveal the formation of free volume in the BF matrix associated with the presence of plasticizers (water and glycerol). The T2 behavior in BFs is consistent with the behavior of spin-lattice relaxation (T1). Our result is the first attempt to characterize using low field 1H NMR technology how all protons in a film matrix behave and to develop correlations between proton mobility and free volume in protein-based BFs plasticized with water and glycerol. PMID:18052122

  15. Nanoantioxidant-driven plasmon enhanced proton-coupled electron transfer.

    PubMed

    Sotiriou, Georgios A; Blattmann, Christoph O; Deligiannakis, Yiannis

    2016-01-14

    Proton-coupled electron transfer (PCET) reactions involve the transfer of a proton and an electron and play an important role in a number of chemical and biological processes. Here, we describe a novel phenomenon, plasmon-enhanced PCET, which is manifested using SiO2-coated Ag nanoparticles functionalized with gallic acid (GA), a natural antioxidant molecule that can perform PCET. These GA-functionalized nanoparticles show enhanced plasmonic response at near-IR wavelengths, due to particle agglomeration caused by the GA molecules. Near-IR laser irradiation induces strong local hot-spots on the SiO2-coated Ag nanoparticles, as evidenced by surface enhanced Raman scattering (SERS). This leads to plasmon energy transfer to the grafted GA molecules that lowers the GA-OH bond dissociation enthalpy by at least 2 kcal mol(-1) and therefore facilitates PCET. The nanoparticle-driven plasmon-enhancement of PCET brings together the so far unrelated research domains of nanoplasmonics and electron/proton translocation with significant impact on applications based on interfacial electron/proton transfer. PMID:26505730

  16. Analyzing and Interpreting NMR Spin-Spin Coupling Constants Using Molecular Orbital Calculations

    ERIC Educational Resources Information Center

    Autschbach, Jochen; Le Guennic, Boris

    2007-01-01

    Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.

  17. Catalytic Olefin Hydroamidation Enabled by Proton-Coupled Electron Transfer

    PubMed Central

    2015-01-01

    Here we report a ternary catalyst system for the intramolecular hydroamidation of unactivated olefins using simple N-aryl amide derivatives. Amide activation in these reactions occurs via concerted proton-coupled electron transfer (PCET) mediated by an excited state iridium complex and weak phosphate base to furnish a reactive amidyl radical that readily adds to pendant alkenes. A series of H-atom, electron, and proton transfer events with a thiophenol cocatalyst furnish the product and regenerate the active forms of the photocatalyst and base. Mechanistic studies indicate that the amide substrate can be selectively homolyzed via PCET in the presence of the thiophenol, despite a large difference in bond dissociation free energies between these functional groups. PMID:26439818

  18. Proton transfer and energy coupling in the bacteriorhodopsin photocycle

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1992-01-01

    A description of the rate constants and the energetics of the elementary reaction steps of the photocycle of bacteriorhodopsin has been helpful in understanding the mechanism of proton transport in this light-driven pump. The evidence suggests a single unbranched reaction sequence, BR-hv----K in equilibrium with L in equilibrium with M1----M2 in equilibrium with N in equilibrium with O----BR, where coupling to the proton-motive force is at the energetically and mechanistically important M1----M2 step. The consequences of site-specific mutations expressed homologously in Halobacterium halobium have revealed characteristics of the Schiff base deprotonation in the L----M1 reaction, the reorientation of the Schiff base from the extracellular to the cytoplasmic side in the M1----M2 reaction, and the reprotonation of the Schiff base in the M2----N reaction.

  19. Proton NMR assignments and regular backbone structure of bovine pancreatic ribonuclease A in aqueous solution

    SciTech Connect

    Robertson, A.D. ); Purisima, E.O. Cornell Univ., Ithaca, NY ); Eastman, M.A.; Scheraga, H.A. )

    1989-07-11

    Proton NMR assignments have been made for 121 of the 124 residues of bovine pancreatic ribonuclease A (RNase A). During the first stage of assignment, COSY and relayed COSY data were used to identify 40 amino acid spin systems belonging to alanine, valine, threonine, isoleucine, and serine residues. Approximately 60 other NH-{alpha}CH-{beta}CH systems were also identified but not assigned to specific amino acid type. NOESY data then were used to connect sequentially neighboring spin systems; approximately 475 of the possible 700 resonances in RNase A were assigned in this way. The authors' assignments agree with those for 20 residues assigned previously. NOESY correlations were used to identify regular backbone structure elements in RNase A, which are very similar to those observed in X-ray crystallographic studies.

  20. In vitro proton NMR study of collagen in human aortic wall.

    PubMed

    Vinée, P; Meurer, B; Constantinesco, A; Kohlberger, B; Hauenstein, K H; Laubenberger, J

    1993-03-01

    The authors relate the findings in the 1H solid state line shape (at 60 MHz) of human aortic walls (n = 12) in native state and after histologically controlled selective lysis of collagen and elastin. An analysis of the line shape shows a composite free induction decay (FID) consisting of a low amplitude (3-7%) fast decaying component (T2 approximately 20 microseconds) and a slow decaying one (T2 > 1 ms). The fast component is identified as the protons of the collagen macromolecules. The second moment computed from the experimental fast component of the FID is in agreement with published studies examining the motional characteristics of collagen by multinuclear NMR employing spin labeling. A theoretical second moment is computed for the collagen macromolecular backbone from the atomic positions in the superhelix. Comparison with the observed experimental values allows determination of the step angle (29 degrees) of the fast rotational motion of the collagen strands along their long axis. PMID:8383787

  1. Proton NMR investigation into the basis for the relatively high redox potential of lignin peroxidase

    SciTech Connect

    Banci, L.; Bertini, I.; Turano, P. ); Ming Tien ); Kirk, T.K. )

    1991-08-15

    Lignin peroxidase shares several structural features with the well-studied horseradish peroxidase and cytochrome c peroxidase but carries a higher redox potential. Here the heme domain of lignin peroxidase and the lignin peroxidase cyanide adduct was examined by {sup 1}H NMR spectroscopy, including nuclear Overhauser effect and two-dimensional measurements, and the findings were compared with those for horseradish peroxidase and cytochrome c peroxidase. Structural information was obtained on the orientation of the heme vinyl and propionate groups and the proximal and distal histidines. The shifts of the {var epsilon}1 proton of the proximal histidine were found to be empirically related to the Fe{sup 3+}/Fe{sup 2+} redox potentials.

  2. Solution NMR Experiment for Measurement of (15)N-(1)H Residual Dipolar Couplings in Large Proteins and Supramolecular Complexes.

    PubMed

    Eletsky, Alexander; Pulavarti, Surya V S R K; Beaumont, Victor; Gollnick, Paul; Szyperski, Thomas

    2015-09-01

    NMR residual dipolar couplings (RDCs) are exquisite probes of protein structure and dynamics. A new solution NMR experiment named 2D SE2 J-TROSY is presented to measure N-H RDCs for proteins and supramolecular complexes in excess of 200 kDa. This enables validation and refinement of their X-ray crystal and solution NMR structures and the characterization of structural and dynamic changes occurring upon complex formation. Accurate N-H RDCs were measured at 750 MHz (1)H resonance frequency for 11-mer 93 kDa (2)H,(15)N-labeled Trp RNA-binding attenuator protein tumbling with a correlation time τc of 120 ns. This is about twice as long as that for the most slowly tumbling system, for which N-H RDCs could be measured, so far, and corresponds to molecular weights of ∼200 kDa at 25 °C. Furthermore, due to the robustness of SE2 J-TROSY with respect to residual (1)H density from exchangeable protons, increased sensitivity at (1)H resonance frequencies around 1 GHz promises to enable N-H RDC measurement for even larger systems. PMID:26293598

  3. Collection of NMR Scalar and Residual Dipolar Couplings Using a Single Experiment.

    PubMed

    Gil-Silva, Leandro F; Santamaría-Fernández, Raquel; Navarro-Vázquez, Armando; Gil, Roberto R

    2016-01-11

    A new DMSO-compatible aligning gel based on cross-linked poly(2-hydroxylethyl methacrylate) (poly-HEMA) has been developed. Due to a significant difference in bulk magnetic susceptibility between the DMSO inside and outside the gel, it is possible to simultaneously collect isotropic and anisotropic NMR data, such as residual dipolar couplings (RDC), in the same NMR tube. RDC-assisted structural analysis of menthol and the alkaloid retrorsine is reported as proof of concept. PMID:26515991

  4. Search for a coupling of the proton spin to gravity

    NASA Astrophysics Data System (ADS)

    Jackson Kimball, Derek; Dudley, Jordan; Li, Yan; Patel, Dilan

    2016-05-01

    We present an overview of progress in our search for a long-range coupling between rubidium (Rb) nuclear spins and the mass of the Earth, which can be interpreted as a search for a long-range monopole-dipole interaction or a spin-gravity coupling. The experiment consists of simultaneous measurement of the spin precession frequencies of overlapping ensembles of Rb-85 and Rb-87 atoms contained within an evacuated, antirelaxation-coated vapor cell. Because of the nuclear structure of Rb-85 and Rb-87, the experiment is particularly sensitive to anomalous spin-dependent interactions of the proton. We have studied a number of important systematic effects related to vector and tensor light shifts, optical pumping effects, the ac and nonlinear Zeeman effects, and magnetic field gradients. We anticipate that our experiment can improve sensitivity to anomalous long-range spin-mass couplings of the proton compared to previous experiments by more than an order of magnitude. Supported by the National Science Foundation under Grant PHY-1307507.

  5. Helical stacking in DNA three-way junctions containing two unpaired pyrimidines: proton NMR studies.

    PubMed Central

    Leontis, N B; Hills, M T; Piotto, M; Ouporov, I V; Malhotra, A; Gorenstein, D G

    1995-01-01

    The proton NMR spectra of DNA three-way junction complexes (TWJ) having unpaired pyrimidines, 5'-TT- and 5'-TC- on one strand at the junction site were assigned from 2D NOESY spectra acquired in H2O and D2O solvents and homonuclear 3D NOESY-TOCSY and 3D NOESY-NOESY in D2O solvent. TWJ are the simplest branched structures found in biologically active nucleic acids. Unpaired nucleotides are common features of such structures and have been shown to stabilize junction formation. The NMR data confirm that the component oligonucleotides assemble to form conformationally homogeneous TWJ complexes having three double-helical, B-form arms. Two of the helical arms stack upon each other. The unpaired pyrimidine bases lie in the minor groove of one of the helices and are partly exposed to solvent. The coaxial stacking arrangement deduced is different from that determined by Rosen and Patel (Rosen, M.A., and D.J. Patel. 1993. Biochemistry. 32:6576-6587) for a DNA three-way junction having two unpaired cytosines, but identical to that suggested by Welch et al. (Welch, J. B., D. R. Duckett, D. M. J. Lilley. 1993. Nucleic Acids Res. 21:4548-4555) on the basis of gel electrophoretic studies of DNA three-way junctions containing unpaired adenosines and thymidines. Images FIGURE 2 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 PMID:7711249

  6. Resolving intermediates in biological proton-coupled electron transfer: a tyrosyl radical prior to proton movement.

    PubMed

    Faller, Peter; Goussias, Charilaos; Rutherford, A William; Un, Sun

    2003-07-22

    The coupling of proton chemistry with redox reactions is important in many enzymes and is central to energy transduction in biology. However, the mechanistic details are poorly understood. Here, we have studied tyrosine oxidation, a reaction in which the removal of one electron from the amino acid is linked to the release of its phenolic proton. Using the unique photochemical properties of photosystem II, it was possible to oxidize the tyrosine at 1.8 K, a temperature at which proton and protein motions are limited. The state formed was detected by high magnetic field EPR as a high-energy radical intermediate trapped in an unprecedentedly electropositive environment. Warming of the protein allows this state to convert to a relaxed, stable form of the radical. The relaxation event occurs at 77 K and seems to involve proton migration and only a very limited movement of the protein. These reactions represent a stabilization process that prevents the back-reaction and determines the reactivity of the radical. PMID:12855767

  7. Resolving intermediates in biological proton-coupled electron transfer: A tyrosyl radical prior to proton movement

    PubMed Central

    Faller, Peter; Goussias, Charilaos; Rutherford, A. William; Un, Sun

    2003-01-01

    The coupling of proton chemistry with redox reactions is important in many enzymes and is central to energy transduction in biology. However, the mechanistic details are poorly understood. Here, we have studied tyrosine oxidation, a reaction in which the removal of one electron from the amino acid is linked to the release of its phenolic proton. Using the unique photochemical properties of photosystem II, it was possible to oxidize the tyrosine at 1.8 K, a temperature at which proton and protein motions are limited. The state formed was detected by high magnetic field EPR as a high-energy radical intermediate trapped in an unprecedentedly electropositive environment. Warming of the protein allows this state to convert to a relaxed, stable form of the radical. The relaxation event occurs at 77 K and seems to involve proton migration and only a very limited movement of the protein. These reactions represent a stabilization process that prevents the back-reaction and determines the reactivity of the radical. PMID:12855767

  8. The Structural Response of Polyelectrolyte Dendrimer toward the Molecular Protonation: The Inconsistence Revealed by SANS and NMR

    SciTech Connect

    Chen, Wei-Ren; Herwig, Kenneth W; Hong, Kunlun; Li, Xin; Liu, Emily; Liu, Yun; Porcar, L.; Shew, Chwen-Yang; Smith, Gregory Scott; Wu, Bin; Liu, Dazhi; Gao, Carrie Y

    2012-01-01

    Polyamidoamine (PAMAM) dendrimers and their charged state in deuterium oxide have been investigated with diffusion NMR and small angle neutron scattering (SANS) techniques. NMR measurement suggests that, upon increasing the molecular protonation by progressive acidification of solutions, significant variation of hydrodynamic radius, calculated by the Stokes-Einstein relation with given surface condition, is observed upon increasing the molecular protonation. However, comparative SANS experiment indicates little dependence of dendrimer global size, in terms of radius of gyration, on molecular protonation. This observed inconsistence indicates the necessity of incorporating the effect of molecular interface modification by dressed counterion, when dynamical measurements are used for determination the structural characteristics of ionic soft colloids even in a dilute enough suspension.

  9. High-resolution proton CRAMPS NMR using narrowband analog filters and postponed data acquisition

    NASA Astrophysics Data System (ADS)

    Wang, Liying; Zhou, Donghua H.

    2013-09-01

    Proton linewidths decrease with increasing magic-angle spinning (MAS) rates. However, without spin dilution by deuteration, even with the fastest MAS rates available today, the narrowest proton linewidths are obtained by using the combined rotation and multiple pulse spectroscopy (CRAMPS) method. Direct observation under windowed CRAMPS typically introduces several tens of times more noise, partly because wideband analog filters (e.g. 5 MHz) must be used or sometimes even bypassed. Here we report that it is possible to keep using narrowband analog filters (about 50 kHz cutoff frequency) in CRAMPS by taking advantage of the time delay caused by the filters, which is inversely proportional to the cutoff frequency. This delay coincides with typical CRAMPS cycle times, enabling acquisition of the data point in the next detection window. The noise of such CRAMPS spectra is only about 5 times larger than MAS-only spectra. This new method allows CRAMPS to be performed on systems that lack wideline hardware (wideband filters and fast ADCs), for example, older spectrometers originally intended for solution NMR.

  10. Histidine side-chain dynamics and protonation monitored by 13C CPMG NMR relaxation dispersion.

    PubMed

    Hass, Mathias A S; Yilmaz, Ali; Christensen, Hans E M; Led, Jens J

    2009-08-01

    The use of 13C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically 13C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for 13C(epsilon1) nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from 15N backbone relaxation measurements. Compared to measurements of backbone nuclei, 13C(epsilon1) dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the 13C(epsilon1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed. PMID:19533375

  11. Amide Proton Solvent Protection in Amylin Fibrils Probed by Quenched Hydrogen Exchange NMR

    PubMed Central

    Alexandrescu, Andrei T.

    2013-01-01

    Amylin is an endocrine hormone that accumulates in amyloid plaques in patients with advanced type 2 diabetes. The amyloid plaques have been implicated in the destruction of pancreatic β-cells, which synthesize amylin and insulin. To better characterize the secondary structure of amylin in amyloid fibrils we assigned the NMR spectrum of the unfolded state in 95% DMSO and used a quenched hydrogen-deuterium exchange technique to look at amide proton solvent protection in the fibrils. In this technique, partially exchanged fibrils are dissolved in 95% DMSO and information about amide proton occupancy in the fibrils is determined from DMSO-denatured monomers. Hydrogen exchange lifetimes at pH 7.6 and 37°C vary between ∼5 h for the unstructured N-terminus to 600 h for amide protons in the two β-strands that form inter-molecular hydrogen bonds between amylin monomers along the length of the fibril. Based on the protection data we conclude that residues A8-H18 and I26-Y37 comprise the two β-strands in amylin fibrils. There is variation in protection within the β-strands, particularly for strand β1 where only residues F15-H18 are strongly protected. Differences in protection appear to be due to restrictions on backbone dynamics imposed by the packing of two-layers of C2-symmetry-related β-hairpins in the protofilament structure, with strand β1 positioned on the surface and β2 in the interior. PMID:23457571

  12. Lactonization and protonation of gluconic acid: a thermodynamicand kinetic study by potentiometry, nmr and esi-ms

    SciTech Connect

    Zhang, Z.; Gibson, P.; Clark, S.B.; Tian, G.; Zanonato, P.; Rao, L.

    2007-01-10

    In acidic aqueous solutions, gluconate protonation is coupled with lactonization of gluconic acid. With the decrease of pC{sub H}, two lactones ({delta}/{gamma}) are sequentially formed. The {delta}-lactone forms more readily than the {gamma}-lactone. In 0.1 M gluconate solutions, if pC{sub H} is above 2.5, only the {delta}-lactone is generated. When pC{sub H} is decreased below 2.0, the formation of the {gamma}-lactone is observable although the {delta}-lactone predominates. At I = 0.1 M NaClO{sub 4} and room temperature, the deprotonation constant of the carboxylic group, using the NMR technique, was determined to be log K{sub a} = 3.30 {+-} 0.02; the {delta}-lactonization constant, by the batch potentiometric titrations, was obtained to be log K{sub L} = - (0.54 {+-} 0.04). Using ESI-MS, the rate constants of the {delta}-lactonization and the hydrolysis at pC{sub H} {approx} 5.0 were estimated to be k{sub 1} = 3.2 x 10{sup -5} s{sup -1} and k{sup -1} = 1.1 x 10{sup -4} s{sup -1}, respectively.

  13. On the Importance of Exchangeable NH Protons in Creatine for the Magnetic Coupling of Creatine Methyl Protons in Skeletal Muscle

    NASA Astrophysics Data System (ADS)

    Kruiskamp, M. J.; Nicolay, K.

    2001-03-01

    The methyl protons of creatine in skeletal muscle exhibit a strong off-resonance magnetization transfer effect. The mechanism of this process is unknown. We previously hypothesized that the exchangeable amide/amino protons of creatine might be involved. To test this the characteristics of the creatine magnetization transfer effect were investigated in excised rat hindleg skeletal muscle that was equilibrated in either H2O or D2O solutions containing creatine. The efficiency of off-resonance magnetization transfer to the protons of mobile creatine in excised muscle was similar to that previously reported in intact muscle in vivo. Equilibrating the isolated muscle in D2O solution had no effect on the magnetic coupling to the immobile protons. It is concluded that exchangeable protons play a negligible role in the magnetic coupling of creatine methyl protons in muscle.

  14. Proton-coupled electron transfer with photoexcited metal complexes.

    PubMed

    Wenger, Oliver S

    2013-07-16

    Proton-coupled electron transfer (PCET) plays a crucial role in many enzymatic reactions and is relevant for a variety of processes including water oxidation, nitrogen fixation, and carbon dioxide reduction. Much of the research on PCET has focused on transfers between molecules in their electronic ground states, but increasingly researchers are investigating PCET between photoexcited reactants. This Account describes recent studies of excited-state PCET with d(6) metal complexes emphasizing work performed in my laboratory. Upon photoexcitation, some complexes release an electron and a proton to benzoquinone reaction partners. Others act as combined electron-proton acceptors in the presence of phenols. As a result, we can investigate photoinduced PCET involving electron and proton transfer in a given direction, a process that resembles hydrogen-atom transfer (HAT). In other studies, the photoexcited metal complexes merely serve as electron donors or electron acceptors because the proton donating and accepting sites are located on other parts of the molecular PCET ensemble. We and others have used this multisite design to explore so-called bidirectional PCET which occurs in many enzymes. A central question in all of these studies is whether concerted proton-electron transfer (CPET) can compete kinetically with sequential electron and proton transfer steps. Short laser pulses can trigger excited-state PCET, making it possible to investigate rapid reactions. Luminescence spectroscopy is a convenient tool for monitoring PCET, but unambiguous identification of reaction products can require a combination of luminescence spectroscopy and transient absorption spectroscopy. Nevertheless, in some cases, distinguishing between PCET photoproducts and reaction products formed by simple photoinduced electron transfer (ET) (reactions that don't include proton transfer) is tricky. Some of the studies presented here deal directly with this important problem. In one case study we

  15. Advanced solid-state NMR characterization of marine dissolved organic matter isolated using the coupled reverse osmosis/electrodialysis method.

    PubMed

    Mao, Jingdong; Kong, Xueqian; Schmidt-Rohr, Klaus; Pignatello, Joseph J; Perdue, E Michael

    2012-06-01

    Advanced (13)C solid-state techniques were employed to investigate the major structural characteristics of two surface-seawater dissolved organic matter (DOM) samples isolated using the novel coupled reverse osmosis/electrodialysis method. The NMR techniques included quantitative (13)C direct polarization/magic angle spinning (DP/MAS) and DP/MAS with recoupled dipolar dephasing, (13)C cross-polarization/total sideband suppression (CP/TOSS), (13)C chemical shift anisotropy filter, CH, CH(2), and CH(n) selection, two-dimensional (1)H-(13)C heteronuclear correlation NMR (2D HETCOR), 2D HETCOR combined with dipolar dephasing, and (15)N cross-polarization/magic angle spinning (CP/MAS). The two samples (Coastal and Marine DOM) were collected at the mouth of the Ogeechee River and in the Gulf Stream, respectively. The NMR results indicated that they were structurally distinct. Coastal DOM contained significantly more aromatic and carbonyl carbons whereas Marine DOM was markedly enriched in alkoxy carbon (e.g., carbohydrate-like moieties). Both samples contained significant amide N, but Coastal DOM had nitrogen bonded to aromatic carbons. Our dipolar-dephased spectra indicated that a large fraction of alkoxy carbons were not protonated. For Coastal DOM, our NMR results were consistent with the presence of the major structural units of (1) carbohydrate-like moieties, (2) lignin residues, (3) peptides or amino sugars, and (4) COO-bonded alkyls. For Marine DOM, they were (1) carbohydrate-like moieties, (2) peptides or amino sugars, and (3) COO-bonded alkyls. In addition, both samples contained significant amounts of nonpolar alkyl groups. The potential sources of the major structural units of DOM were discussed in detail. Nonprotonated O-alkyl carbon content was proposed as a possible index of humification. PMID:22553962

  16. Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

    SciTech Connect

    Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2015-11-21

    Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency proton donor-acceptor vibrational modes. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term in the framework of the cumulant expansion framework may significantly impact the rate constants at high temperatures for proton transfer interfaces with soft proton donor-acceptor modes that are associated with small force constants and weak hydrogen bonds. The effects of the quadratic term may also become significant in these regimes when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant. In this case, however, the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances sampled. The effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances. Additionally, the rigorous relation between the cumulant expansion and thermal averaging approaches is clarified. In particular, the cumulant expansion rate constant includes effects from dynamical interference between the proton donor-acceptor and solvent motions and becomes equivalent to the thermally averaged rate constant when these dynamical effects are neglected. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton

  17. Insights into Proton-Coupled Electron Transfer from Computation

    NASA Astrophysics Data System (ADS)

    Provorse, Makenzie R.

    Proton-coupled electron transfer (PCET) is utilized throughout Nature to facilitate essential biological processes, such as photosynthesis, cellular respiration, and DNA replication and repair. The general approach to studying PCET processes is based on a two-dimensional More O'Ferrall-Jencks diagram in which electron transfer (ET) and proton transfer (PT) occur in a sequential or concerted fashion. Experimentally, it is difficult to discern the contributing factors of concerted PCET mechanisms. Several theoretical approaches have arisen to qualitatively and quantitatively investigate these reactions. Here, we present a multistate density functional theory (MSDFT) method to efficiently and accurately model PCET mechanisms. The MSDFT method is validated against experimental and computational data previously reported on an isoelectronic series of small molecule self-exchange hydrogen atom transfer reactions and a model complex specifically designed to study long-range ET through a hydrogen-bonded salt-bridge interface. Further application of this method to the hydrogen atom abstraction of ascorbate by a nitroxyl radical demonstrates the sensitivity of the thermodynamic and kinetic properties to solvent effects. In particular, the origin of the unusual kinetic isotope effect is investigated. Lastly, the MSDFT is employed in a combined quantum mechanical/molecular mechanical (QM/MM) approach to explicitly model PCET in condensed phases.

  18. Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

    SciTech Connect

    Soudackov, Alexander; Hammes-Schiffer, Sharon

    2015-11-17

    Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency regimes for the proton donor-acceptor vibrational mode. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term does not significantly impact the rate constants derived using the cumulant expansion approach in any of the regimes studied. The effects of the quadratic term may become significant when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant, however, particularly at high temperatures and for proton transfer interfaces with extremely soft proton donor-acceptor modes that are associated with extraordinarily weak hydrogen bonds. Even with the thermal averaging procedure, the effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances, and the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes. We are grateful for support from National Institutes of Health Grant GM056207 (applications to enzymes) and the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy

  19. Proton-Coupled Electron Transfer: Moving Together and Charging Forward

    PubMed Central

    2016-01-01

    Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa’s for molecular electrocatalysts, as well as insights into linear correlations and non-innocent ligands, are also described. In addition, computational methods for simulating the nonadiabatic dynamics of photoexcited PCET are discussed. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future. PMID:26110700

  20. Gating Topology of the Proton-Coupled Oligopeptide Symporters

    PubMed Central

    Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian; Solcan, Nicolae; Dijkman, Patricia M.; Lyons, Joseph A.; Kwok, Jane; Caffrey, Martin; Watts, Anthony; Forrest, Lucy R.; Newstead, Simon

    2015-01-01

    Summary Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport. PMID:25651061

  1. Proton-Coupled Electron Transfer: Moving Together and Charging Forward.

    PubMed

    Hammes-Schiffer, Sharon

    2015-07-22

    Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa's for molecular electrocatalysts, as well as insights into linear correlations and non-innocent ligands, are also described. In addition, computational methods for simulating the nonadiabatic dynamics of photoexcited PCET are discussed. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future. PMID:26110700

  2. Influence of the incorporation of fibers in biscuit dough on proton mobility characterized by time domain NMR.

    PubMed

    Serial, M R; Blanco Canalis, M S; Carpinella, M; Valentinuzzi, M C; León, A E; Ribotta, P D; Acosta, R H

    2016-02-01

    The effect of fiber addition on the distribution and mobility of protons in biscuits is studied by using low resolution time domain nuclear magnetic resonance (TD-NMR). The proportion of flour is reduced in order to incorporate inulin and oat fiber. NMR temperature dependent experiments are carried out in order to gain insight on the processes occurring in biscuit baking. Proton populations were identified measuring spin-spin relaxation times (T2). The major change in the relaxation profiles upon incorporation of fibers corresponds to mobile water molecules, which appear to be related to dough spreading behavior and biscuit quality. Biscuit samples baked in a commercial oven were studied by two dimensional spin-lattice/spin-spin (T1-T2) relaxation maps. The T1/T2 ratio is used as an indicator of the population mobility, where changes in the mobility of water in contact with flour components as starch, proteins and pentosans are observed. PMID:26304434

  3. Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR.

    PubMed Central

    Zhang, Y. Z.; Paterson, Y.; Roder, H.

    1995-01-01

    In an effort to develop a more versatile quenched hydrogen exchange method for studies of peptide conformation and protein-ligand interactions, the mechanism of amide proton exchange for model peptides in DMSO-D2O mixtures was investigated by NMR methods. As in water, H-D exchange rates in the presence of 90% or 95% DMSO exhibit characteristic acid- and base-catalyzed processes and negligible water catalysis. However, the base-catalyzed rate is suppressed by as much as four orders of magnitude in 95% DMSO. As a result, the pH at which the exchange rate goes through a minimum is shifted up by about two pH units and the minimum exchange rate is approximately 100-fold reduced relative to that in D2O. The solvent-dependent decrease in base-catalyzed exchange rates can be attributed primarily to a large increase in pKa values for the NH group, whereas solvent effects on pKW seem less important. Addition of toluene and cyclohexane resulted in improved proton NMR chemical shift dispersion. The dramatic reduction in exchange rates observed in the solvent mixture at optimal pH makes it possible to apply 2D NMR for NH exchange measurements on peptides under conditions where rates are too rapid for direct NMR analysis. To test this solvent-quenching method, melittin was exchanged in D2O (pH 3.2, 12 degrees C), aliquots were quenched by rapid freezing, lyophilized, and dissolved in quenching buffer (70% DMSO, 25% toluene, 4% D2O, 1% cyclohexane, 75 mM dichloroacetic acid) for NMR analysis. Exchange rates for 21 amide protons were measured by recording 2D NMR spectra on a series of samples quenched at different times. The results are consistent with a monomeric unfolded conformation of melittin at acidic pH. The ability to trap labile protons by solvent quenching makes it possible to extend amide protection studies to peptide ligands or labile protons on the surface of a protein involved in macromolecular interactions. PMID:7613478

  4. Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance ((1) H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS).

    PubMed

    Paiva, C; Amaral, A; Rodriguez, M; Canyellas, N; Correig, X; Ballescà, J L; Ramalho-Santos, J; Oliva, R

    2015-05-01

    The objective of this study was to contribute to the first comprehensive metabolomic characterization of the human sperm cell through the application of two untargeted platforms based on proton nuclear magnetic resonance ((1) H-NMR) spectroscopy and gas chromatography coupled to mass spectrometry (GC-MS). Using these two complementary strategies, we were able to identify a total of 69 metabolites, of which 42 were identified using NMR, 27 using GC-MS and 4 by both techniques. The identity of some of these metabolites was further confirmed by two-dimensional (1) H-(1) H homonuclear correlation spectroscopy (COSY) and (1) H-(13) C heteronuclear single-quantum correlation (HSQC) spectroscopy. Most of the metabolites identified are reported here for the first time in mature human spermatozoa. The relationship between the metabolites identified and the previously reported sperm proteome was also explored. Interestingly, overrepresented pathways included not only the metabolism of carbohydrates, but also of lipids and lipoproteins. Of note, a large number of the metabolites identified belonged to the amino acids, peptides and analogues super class. The identification of this initial set of metabolites represents an important first step to further study their function in male gamete physiology and to explore potential reasons for dysfunction in future studies. We also demonstrate that the application of NMR and MS provides complementary results, thus constituting a promising strategy towards the completion of the human sperm cell metabolome. PMID:25854681

  5. Assignments of proton populations in dough and bread using NMR relaxometry of starch, gluten, and flour model systems.

    PubMed

    Bosmans, Geertrui M; Lagrain, Bert; Deleu, Lomme J; Fierens, Ellen; Hills, Brian P; Delcour, Jan A

    2012-05-30

    Starch-water, gluten-water, and flour-water model systems as well as straight-dough bread were investigated with (1)H NMR relaxometry using free induction decay and Carr-Purcell-Meiboom-Gill pulse sequences. Depending on the degree of interaction between polymers and water, different proton populations could be distinguished. The starch protons in the starch-water model gain mobility owing to amylopectin crystal melting, granule swelling, and amylose leaching, whereas water protons lose mobility due to increased interaction with starch polymers. Heating of the gluten-water sample induces no pronounced changes in proton distributions. Heating changes the proton distributions of the flour-water and starch-water models in a similar way, implying that the changes are primarily attributable to starch gelatinization. Proton distributions of the heated flour-water model system and those of fresh bread crumb are very similar. This allows identifying the different proton populations in bread on the basis of the results from the model systems. PMID:22553963

  6. Single-Quantum Coherence Filter for Strongly Coupled Spin Systems for Localized 1H NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Trabesinger, Andreas H.; Mueller, D. Christoph; Boesiger, Peter

    2000-08-01

    A pulse sequence for localized in vivo1H NMR spectroscopy is presented, which selectively filters single-quantum coherence built up by strongly coupled spin systems. Uncoupled and weakly coupled spin systems do not contribute to the signal output. Analytical calculations using a product operator description of the strongly coupled AB spin system as well as in vitro tests demonstrate that the proposed filter produces a signal output for a strongly coupled AB spin system, whereas the resonances of a weakly coupled AX spin system and of uncoupled spins are widely suppressed. As a potential application, the detection of the strongly coupled AA‧BB‧ spin system of taurine at 1.5 T is discussed.

  7. Visualizing Unresolved Scalar Couplings by Real-Time J-Upscaled NMR

    PubMed Central

    2015-01-01

    Scalar coupling patterns contain a wealth of structural information. The determination, especially of small scalar coupling constants, is often prevented by merging the splittings with the signal line width. Here we show that real-time J-upscaling enables the visualization of unresolved coupling constants in the acquisition dimension of one-dimensional (1D) or multidimensional NMR spectra. This technique, which works by introducing additional scalar coupling evolution delays within the recording of the FID (free induction decay), not only stretches the recorded coupling patterns but also actually enhances the resolution of multiplets, by reducing signal broadening by magnetic field inhomogeneities during the interrupted data acquisition. Enlarging scalar couplings also enables their determination in situations where the spectral resolution is limited, such as in the acquisition dimension of heteronuclear broadband decoupled HSQC (heteronuclear single quantum correlation) spectra. PMID:25837306

  8. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.

    PubMed

    Juen, Michael Andreas; Wunderlich, Christoph Hermann; Nußbaumer, Felix; Tollinger, Martin; Kontaxis, Georg; Konrat, Robert; Hansen, D Flemming; Kreutz, Christoph

    2016-09-19

    In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids. PMID:27533469

  9. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    NASA Astrophysics Data System (ADS)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  10. Scalar Relativistic Computations and Localized Orbital Analyses of Nuclear Hyperfine Coupling and Paramagnetic NMR Chemical Shifts

    SciTech Connect

    Aquino, Fredy W.; Pritchard, Ben; Autschbach, Jochen

    2012-02-14

    A method is reported by which calculated hyperfine coupling constants (HFCCs) and paramagnetic NMR (pNMR) chemical shifts can be analyzed in a chemically intuitive way by decomposition into contributions from localized molecular orbitals (LMOs). A new module for density functional calculations with nonhybrid functionals, global hybrids, and range-separated hybrids, utilizing the two-component relativistic zeroth-order regular approximation (ZORA), has been implemented in the parallel open-source NWChem quantum chemistry package. Benchmark results are reported for a test set of few-atom molecules with light and heavy elements. Finite nucleus effects on ¹⁹⁹Hg HFCCs are shown to be on the order of -11 to -15%. A proof of concept for the LMO analysis is provided for the metal and fluorine HFCCs of TiF₃ and NpF₆. Calculated pNMR chemical shifts are reported for the 2-methylphenyl-t-butylnitroxide radical and for five cyclopentadienyl (Cp) sandwich complexes with 3d metals. Nickelocene and vanadocene carbon pNMR shifts are analyzed in detail, demonstrating that the large carbon pNMR shifts calculated as +1540 for Ni (exptl.: +1514) and -443 for V (exptl.: -510) are caused by different spin-polarization mechanisms. For Ni, Cp to Ni π back-donation dominates the result, whereas for vanadocene, V to Cp σ donation with relaxation of the carbon 1s shells can be identified as the dominant mechanism.

  11. Two-pulse NMR techniques for studying proton-unpaired electron interactions in coals and chars

    NASA Astrophysics Data System (ADS)

    Barton, W. A.; Lynch, L. J.

    The time-domain NMR signals stimulated in solids by two-pulse sequences of the form 90°- τ- βφ, where β is the angle of rotation and φ the relative phase of the second pulse which is separated from the initial 90° pulse by a time τ, can be influenced by the presence of a second spin species and therefore, in principle, can yield information on the separate contributions, M2II and M2IS, of like- and unlike-spin interactions to the Van Vleck second moment M2I of the resonant spins. The validity of the standard operator formalism for predicting the transverse magnetization signals thus produced in homogeneous solids by the 90°- τ-90 φ° and 90°- τ-180 φ° ( φ = 0° and 90°) sequences is discussed and the effects of pulse duration are briefly outlined. The time-series expansions yielded by the operator formalism for these signals are reviewed with emphasis on the effects of unlike-spin interactions, and a useful difference signal is discussed. The potential for application of these two-pulse techniques to protons in heterogeneous solids such as coals, in which unpaired electrons constitute the second spin species, is considered and experimentally assessed. Semiquantitative estimates of M2IS are made for protons in diphenyl picryl hydrazyl (DPPH) and several coals and chars at room temperature from measurements of the amplitude of the 90°- τ-90° 0 ° transient signal at small τ and of the initial rate of attenuation of the 90°- τ-90 90°° solid echo with increasing τ. It is found that (i) organic radicals and paramagnetic ions produce relatively small M2IS values, a result which limits the usefulness of this approach to studying unpaired electron properties of coals and chars; (ii) the M2II values deduced from these results and calculations of M2I follow expected trends; and (iii) only specimens containing small particles of magnetically ordered material give rise to rapidly decaying time-domain signals and a well-defined 90°- τ-180 90°° spin

  12. Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study.

    PubMed

    Barbieri, Christopher M; Pilch, Daniel S

    2006-02-15

    The binding of aminoglycoside antibiotics to a broad range of macromolecular targets is coupled to protonation of one or more of the amino groups that typify this class of drugs. Determining how and to what extent this linkage influences the energetics of the aminoglycoside-macromolecule binding reaction requires a detailed understanding of the thermodynamics associated with the protonation equilibria of the aminoglycoside amino groups. In recognition of this need, a calorimetric- and NMR-based approach for obtaining the requisite thermodynamic information is presented using paromomycin as the model aminoglycoside. Temperature- and pH-dependent 15N NMR studies provide pK(a) values for the five paromomycin amino groups, as well as the temperature dependence of these pK(a) values. These studies also indicate that the observed pK(a) values associated with the free base form of paromomycin are lower in magnitude than the corresponding values associated with the sulfate salt form of the drug. This difference in pK(a) is due to drug interactions with the sulfate counterions at the high drug concentrations (> or = 812 mM) used in the 15N NMR studies. Isothermal titration calorimetry studies conducted at drug concentrations < or = 45 microM reveal that the extent of paromomycin protonation linked to the binding of the drug to its pharmacologically relevant target, the 16 S rRNA A-site, is consistent with the pK(a) values of the free base and not the sulfate salt form of the drug. Temperature- and pH-dependent isothermal titration calorimetry studies yield exothermic enthalpy changes (deltaH) for protonation of the five paromomycin amino groups, as well as positive heat capacity changes (deltaC(p)) for three of the five amino groups. Regarded as a whole, the results presented here represent an important first step toward establishing a thermodynamic database that can be used to predict how aminoglycoside-macromolecule binding energetics will be influenced by conditions such

  13. A General Method for Extracting Individual Coupling Constants from Crowded (1)H NMR Spectra.

    PubMed

    Sinnaeve, Davy; Foroozandeh, Mohammadali; Nilsson, Mathias; Morris, Gareth A

    2016-01-18

    Couplings between protons, whether scalar or dipolar, provide a wealth of structural information. Unfortunately, the high number of (1)H-(1)H couplings gives rise to complex multiplets and severe overlap in crowded spectra, greatly complicating their measurement. Many different methods exist for disentangling couplings, but none approaches optimum resolution. Here, we present a general new 2D J-resolved method, PSYCHEDELIC, in which all homonuclear couplings are suppressed in F2, and only the couplings to chosen spins appear, as simple doublets, in F1. This approaches the theoretical limit for resolving (1)H-(1)H couplings, with close to natural linewidths and with only chemical shifts in F2. With the same high sensitivity and spectral purity as the parent PSYCHE pure shift experiment, PSYCHEDELIC offers a robust method for chemists seeking to exploit couplings for structural, conformational, or stereochemical analyses. PMID:26636773

  14. Solid-State NMR Investigation of the Conformation, Proton Conduction, and Hydration of the Influenza B Virus M2 Transmembrane Proton Channel.

    PubMed

    Williams, Jonathan K; Tietze, Daniel; Lee, Myungwoon; Wang, Jun; Hong, Mei

    2016-07-01

    Together with the influenza A virus, influenza B virus causes seasonal flu epidemics. The M2 protein of influenza B (BM2) forms a tetrameric proton-conducting channel that is important for the virus lifecycle. BM2 shares little sequence homology with AM2, except for a conserved HxxxW motif in the transmembrane (TM) domain. Unlike AM2, no antiviral drugs have been developed to block the BM2 channel. To elucidate the proton-conduction mechanism of BM2 and to facilitate the development of BM2 inhibitors, we have employed solid-state NMR spectroscopy to investigate the conformation, dynamics, and hydration of the BM2 TM domain in lipid bilayers. BM2 adopts an α-helical conformation in lipid membranes. At physiological temperature and low pH, the proton-selective residue, His19, shows relatively narrow (15)N chemical exchange peaks for the imidazole nitrogens, indicating fast proton shuttling that interconverts cationic and neutral histidines. Importantly, pH-dependent (15)N chemical shifts indicate that His19 retains the neutral population to much lower pH than His37 in AM2, indicating larger acid-dissociation constants or lower pKa's. We attribute these dynamical and equilibrium differences to the presence of a second titratable histidine, His27, which may increase the proton-dissociation rate of His19. Two-dimensional (1)H-(13)C correlation spectra probing water (1)H polarization transfer to the peptide indicates that the BM2 channel becomes much more hydrated at low pH than at high pH, particularly at Ser12, indicating that the pore-facing serine residues in BM2 mediate proton relay to the proton-selective histidine. PMID:27286559

  15. Using magnetic coupling to implement 1H, 19F, 13C experiments in routine high resolution NMR probes

    NASA Astrophysics Data System (ADS)

    Bowyer, Paul; Finnigan, Jim; Marsden, Brian; Taber, Bob; Zens, Albert

    2015-12-01

    We report in this paper the design of 1H, 19F, 13C circuitry using magnetic coupling which can do on demand experiments where one of the three nuclei is observed and the other two are decoupled. The implementation of this circuitry in routine NMR probes is compared with capacitive coupling methods where it was found that by using magnetic coupling the performance of the routine NMR probe was not impacted by the addition of this circuitry. It is surmised that using this type of circuitry would be highly desirable for those chemists doing routine 19F NMR.

  16. Synthetic Applications of Proton-Coupled Electron Transfer.

    PubMed

    Gentry, Emily C; Knowles, Robert R

    2016-08-16

    Redox events in which an electron and proton are exchanged in a concerted elementary step are commonly referred to as proton-coupled electron transfers (PCETs). PCETs are known to operate in numerous important biological redox processes, as well as recent inorganic technologies for small molecule activation. These studies suggest that PCET catalysis might also function as a general mode of substrate activation in organic synthesis. Over the past three years, our group has worked to advance this hypothesis and to demonstrate the synthetic utility of PCET through the development of novel catalytic radical chemistries. The central aim of these efforts has been to demonstrate the ability of PCET to homolytically activate a wide variety of common organic functional groups that are energetically inaccessible using known molecular H atom transfer catalysts. To do so, we made use of a simple formalism first introduced by Mayer and co-workers that allowed us to predict the thermodynamic capacity of any oxidant/base or reductant/acid pair to formally add or remove H· from a given substrate. With this insight, we were able to rationally select catalyst combinations thermodynamically competent to homolyze the extraordinarily strong E-H σ-bonds found in many common protic functional groups (BDFEs > 100 kcal/mol) or to form unusually weak bonds to hydrogen via the reductive action of common organic π-systems (BDFEs < 35 kcal/mol). These ideas were reduced to practice through the development of new catalyst systems for reductive PCET activations of ketones and oxidative PCET activation of amide N-H bonds to directly furnish reactive ketyl and amidyl radicals, respectively. In both systems, the reaction outcomes were found to be successfully predicted using the effective bond strength formalism, suggesting that these simple thermochemical considerations can provide useful and actionable insights into PCET reaction design. The ability of PCET catalysis to control

  17. Proton-Coupled Electron Transfer: Moving Together and Charging Forward

    SciTech Connect

    Hammes-Schiffer, Sharon

    2015-06-25

    Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa’s for molecular electrocatalysts, as well as methods for simulating the nonadiabatic dynamics of photoinduced processes, are also described. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future. The work described herein was supported by National Science Foundation Grant CHE-13-61293 (theory development), National Institutes of Health Grant GM056207 (soybean lipoxygenase), Center for Chemical Innovation of the National Science Foundation Solar Fuels Grant CHE-1305124 (cobalt catalysts), Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences (nickel catalysts), and Air Force Office of Scientific Research Award No. FA9550-14-1-0295 (photoinduced PCET).

  18. Improving the Mass-Limited Performance of Routine NMR Probes using Coupled Coils.

    PubMed

    Marsden, Brian; Lim, Victor; Taber, Bob; Zens, Albert

    2016-07-01

    We report a method to convert, on demand, a general use dual-broadband probe to a high performance mass-limited probe for both high band and low band nuclei. This technology uses magnetic coupling of inductors to achieve this capability. The method offers a cost effective way of increasing the performance of routine NMR probes without having to change probes or increase the overall foot print of the spectrometer. PMID:27155588

  19. Improving the Mass-Limited Performance of Routine NMR Probes using Coupled Coils

    NASA Astrophysics Data System (ADS)

    Marsden, Brian; Lim, Victor; Taber, Bob; Zens, Albert

    2016-07-01

    We report a method to convert, on demand, a general use dual-broadband probe to a high performance mass-limited probe for both high band and low band nuclei. This technology uses magnetic coupling of inductors to achieve this capability. The method offers a cost effective way of increasing the performance of routine NMR probes without having to change probes or increase the overall foot print of the spectrometer.

  20. The HN(COCA)HAHB NMR experiment for the stereospecific assignment of Hbeta-protons in non-native states of proteins.

    PubMed

    Hähnke, Martin J; Richter, Christian; Heinicke, Friederike; Schwalbe, Harald

    2010-01-27

    (3)J(H(alpha),H(beta))-coupling constants deliver precious information on the population of the three favored chi(1)-rotamers in unfolded states of proteins. Here, a novel pulse sequence, tailored toward the NMR analysis of non-native states of proteins, the HN(COCA)HAHB experiment, is developed to measure (3)J(H(alpha),H(beta)). In four subsequent INEPT steps, magnetization is transferred from H(N) to H(alpha). In a COSY-like magnetization transfer step, dephasing of magnetization on H(alpha) is quantified to determine the (3)J(H(alpha),H(beta))-coupling constants. Analysis of the measured homonuclear coupling constants, together with measurement of heteronuclear (3)J(N,C(gamma))- and (3)J(C',C(gamma))-coupling constants, allows stereospecific assignment of the two diastereotopic H(beta)-protons even in unfolded states of proteins, and the derivation of populations according to a Pachler-type analysis. PMID:20039672

  1. Measurement of nuclear magnetic dipole—dipole couplings in magic angle spinning NMR

    NASA Astrophysics Data System (ADS)

    Tycko, Robert; Dabbagh, Gary

    1990-10-01

    We describe a method for measuring nuclear magnetic dipole—dipole couplings in NMR spectra of solids undergoing rapid magic angle spinning (MAS). We show in theory, simulations, and experiments that the couplings, which are averaged out by MAS alone, can be recovered by applying simple resonant radiofrequency pulse sequences in synchrony with the sample rotation. Experimental 13C dipolar powder pattern spectra of polycrystalline ( 13CH 3) 2C(OH)SO 3Na obtained in a two-dimensional experiment based on this method are presented. The method provides a means of determining internuclear distances in polycrystalline and noncrystalline solids while retaining the high resolution and sensitivity afforded by MAS.

  2. Novel macrocyclic carriers for proton-coupled liquid membrane transport. Final report

    SciTech Connect

    Lamb, J.D.; Izatt, R.M.; Bradshaw, J.S.; Shirts, R.B.

    1996-08-24

    The objective of this research program is to elucidate the chemical principles which are responsible for the cation selectivity and permeability of liquid membranes containing macrocyclic carriers. Several new macrocyclic carriers were synthesized during the last three year period. In addition, new, more convenient synthetic routes were achieved for several nitrogen-containing bicyclic and tricyclic macrocycles. The cation binding properties of these macrocycles were investigated by potentiometric titration, calorimetric titration, solvent extraction and NMR techniques. In addition, hydrophobic macrocycles were incorporated into dual hollow fiber and other membrane systems to investigate their membrane performance, especially in the proton-coupled transport mode. A study of the effect of methoxyalkyl macrocycle substituents on metal ion transport was completed. A new calorimeter was constructed which made it possible to study the thermodynamics of macrocycle-cation binding to very high temperatures. Measurements of thermodynamic data for the interaction of crown ethers with alkali and alkaline earth cations were achieved to 473 K. Molecular modeling work was begun for the first time on this project and fundamental principles were identified and developed for the establishment of working models in the future.

  3. Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping.

    PubMed

    Dona, Anthony C; Jiménez, Beatriz; Schäfer, Hartmut; Humpfer, Eberhard; Spraul, Manfred; Lewis, Matthew R; Pearce, Jake T M; Holmes, Elaine; Lindon, John C; Nicholson, Jeremy K

    2014-10-01

    Proton nuclear magnetic resonance (NMR)-based metabolic phenotyping of urine and blood plasma/serum samples provides important prognostic and diagnostic information and permits monitoring of disease progression in an objective manner. Much effort has been made in recent years to develop NMR instrumentation and technology to allow the acquisition of data in an effective, reproducible, and high-throughput approach that allows the study of general population samples from epidemiological collections for biomarkers of disease risk. The challenge remains to develop highly reproducible methods and standardized protocols that minimize technical or experimental bias, allowing realistic interlaboratory comparisons of subtle biomarker information. Here we present a detailed set of updated protocols that carefully consider major experimental conditions, including sample preparation, spectrometer parameters, NMR pulse sequences, throughput, reproducibility, quality control, and resolution. These results provide an experimental platform that facilitates NMR spectroscopy usage across different large cohorts of biofluid samples, enabling integration of global metabolic profiling that is a prerequisite for personalized healthcare. PMID:25180432

  4. Thermal coupling of protons and neutral hydrogen with anisotropic temperatures in the fast solar wind

    NASA Astrophysics Data System (ADS)

    Allen, Lorraine A.; Habbal, Shadia R.; Li, Xing

    2000-10-01

    The thermal coupling between the neutral hydrogen and protons in the inner corona is explored by extending the study of Allenet al. [1998] to include anisotropic proton temperature to determine what the neutral hydrogen Ly α spectral line measurements reveal about the proton temperature, temperature anisotropy, and outflow velocity in the fast solar wind. The anisotropic proton temperature is produced by ion cyclotron resonant interaction of protons with high-frequency waves, produced by a nonlinear cascade at the Kolmogorov dissipation rate from dominant lower-frequency Alfvén waves. As a result of the coupling between the respective parallel and perpendicular components of the neutral hydrogen and proton temperatures, a greater temperature anisotropy in the neutral hydrogen develops as compared to the case when the proton temperature is isotropic. The neutral hydrogen and proton effective temperatures (Teff), incorporating both random and wave motions of the particles, and outflow velocities, are comparable below ~3Rs. Neutral hydrogen anisotropy ratios, TH(eff)/T∥, ~4 below 3Rs are readily attained, in agreement with observations. Below ~3Rs, these reflect the proton anisotropy ratio. For plasma conditions typical of the fast solar wind, these results imply that the measured Ly α spectral line profiles, from which the neutral hydrogen temperature, anisotropy ratio, and outflow velocity are inferred, are equivalent to measurements of protons below ~3Rs. Beyond this distance the width of the measured Ly α spectral lines provides a lower limit to the proton effective temperature and temperature anisotropy in the inner corona.

  5. Multicomponent analysis of radiolytic products in human body fluids using high field proton nuclear magnetic resonance (NMR) spectroscopy

    NASA Astrophysics Data System (ADS)

    Grootveld, Martin C.; Herz, Herman; Haywood, Rachel; Hawkes, Geoffrey E.; Naughton, Declan; Perera, Anusha; Knappitt, Jacky; Blake, David R.; Claxson, Andrew W. D.

    1994-05-01

    High field proton Hahn spin-echo nuclear magnetic resonance (NMR) spectroscopy has been employed to investigate radiolytic damage to biomolecules present in intact human body fluids. γ-Radiolysis of healthy or rheumatoid human serum (5.00 kGy) in the presence of atmospheric O 2 gave rise to reproducible elevations in the concentration of NMR-detectable acetate which are predominantly ascribable to the prior oxidation of lactate to pyruvate by hydroxyl radical (·OH) followed by oxidative decarboxylation of pyruvate by radiolytically-generated hydrogen peroxide (H 2O 2) and/or further ·OH radical. Increases in the serum levels of non-protein-bound, low-molecular-mass components such as citrate and glutamine were also observed subsequent to γ-radiolysis, an observation which may reflect their mobilisation from protein binding-sites by ·OH radical, superoxide anion and/or H 2O 2. Moreover, substantial radiolytically-mediated elevations in the concentration of serum formate were also detectable. In addition to the above modifications, γ-radiolysis of inflammatory knee-joint synovial fluid (SF) generated a low-molecular-mass oligosaccharide species derived from the radiolytic fragmentation of hyaluronate. The radiolytically-mediated production of acetate in SF samples was markedly greater than that observed in serum samples, a consequence of the much higher levels of ·OH radical-scavenging lactate present. Indeed, increases in SF acetate concentration were detectable at doses as low as 48 Gy. We conclude that high field proton NMR analysis provides much useful information regarding the relative radioprotectant abilities of endogenous components and the nature, status and levels of radiolytic products generated in intact biofluids. We also suggest that NMR-detectable radiolytic products with associated toxicological properties (e.g. formate) may play a role in contributing to the deleterious effects observed following exposure of living organisms to sources of

  6. Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect.

    PubMed Central

    Mellema, J R; Haasnoot, C A; van der Marel, G A; Wille, G; van Boeckel, C A; van Boom, J H; Altona, C

    1983-01-01

    Proton NMR spectra of a covalently linked self-complementary RNA X DNA hybrid, r(GCG)-d(TATACGC), are recorded in H2O and D2O. Imino proton resonances as well as the non-exchangeable base and H-1' resonances are unambiguously assigned by means of nuclear. Overhauser effect measurements. Additional information was obtained by 31P NMR and circular dichroism spectra. The RNA parts in the duplex attain full conformational purity and adopt the usual A-RNA conformation. The DNA residues opposite the RNA tract do not adopt an A-type structure completely. Their respective sugar rings still appear to possess a certain conformational freedom. The same holds true for the central d(-TATA-) sequence which forms a DNA X DNA duplex. There appears to be a structural break in this part: the first two residues, T(4) and A(5), are clearly influenced by the adjacent RNA structure, whereas residues T(6) and A(7) behave quite similar to what usually is found in DNA duplexes in aqueous solution. PMID:6193486

  7. Rapid proton-detected NMR assignment for proteins with fast magic angle spinning.

    PubMed

    Barbet-Massin, Emeline; Pell, Andrew J; Retel, Joren S; Andreas, Loren B; Jaudzems, Kristaps; Franks, W Trent; Nieuwkoop, Andrew J; Hiller, Matthias; Higman, Victoria; Guerry, Paul; Bertarello, Andrea; Knight, Michael J; Felletti, Michele; Le Marchand, Tanguy; Kotelovica, Svetlana; Akopjana, Inara; Tars, Kaspars; Stoppini, Monica; Bellotti, Vittorio; Bolognesi, Martino; Ricagno, Stefano; Chou, James J; Griffin, Robert G; Oschkinat, Hartmut; Lesage, Anne; Emsley, Lyndon; Herrmann, Torsten; Pintacuda, Guido

    2014-09-01

    Using a set of six (1)H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5-30 kDa proteins. The approach relies on perdeuteration, amide (2)H/(1)H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary (13)C/(15)N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR. PMID:25102442

  8. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles

    SciTech Connect

    Xue, Junfeng; Isern, Nancy G.; Ewing, R James; Liyu, Andrey V.; Sears, Jesse A.; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R.; Ahring, Birgitte K.; Majors, Paul D.

    2014-06-20

    An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequency of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.

  9. First acceleration of a proton beam in a side coupled drift tube linac

    NASA Astrophysics Data System (ADS)

    Ronsivalle, C.; Picardi, L.; Ampollini, A.; Bazzano, G.; Marracino, F.; Nenzi, P.; Snels, C.; Surrenti, V.; Vadrucci, M.; Ambrosini, F.

    2015-07-01

    We report the first experiment aimed at the demonstration of low-energy protons acceleration by a high-efficiency S-band RF linear accelerator. The proton beam has been accelerated from 7 to 11.6 MeV by a 1 meter long SCDTL (Side Coupled Drift Tube Linac) module powered with 1.3 MW. The experiment has been done in the framework of the Italian TOP-IMPLART (Oncological Therapy with Protons-Intensity Modulated Proton Therapy Linear Accelerator for Radio-Therapy) project devoted to the realization of a proton therapy centre based on a proton linear accelerator for intensity modulated cancer treatments to be installed at IRE-IFO, the largest oncological hospital in Rome. It is the first proton therapy facility employing a full linear accelerator scheme based on high-frequency technology.

  10. 1H NMR study of proton motion in hydrogen-bonded chain in Mannich base of 5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol

    NASA Astrophysics Data System (ADS)

    Wojciechowski, G.; Rozwadowski, Z.; Dziembowska, T.; Brzezinski, B.

    2001-01-01

    5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol was synthesized and the collective proton motion in two intramolecular hydrogen bonds was studied by 1H and 13C NMR as well as by FTIR spectroscopy in chloroform, acetonitrile and chloroform containing traces of water solutions. In dry chloroform, always, two separated proton signals for the two OH groups were observed. If traces of water were present at room temperature in the chloroform solution only one signal for the two OH protons was found. With decreasing temperature the collective proton motion, indicated by continuous absorption in the FTIR spectrum, was interrupted and two separate signals appeared in the 1H NMR spectrum. In acetonitrile the collective proton motion in the two intramolecular hydrogen-bonded system observed at room temperature vanished with decreasing temperature and finally only a cooperative hydrogen-bonded system, like in the solid state, was observed.

  11. Experimental study of resolution of proton chemical shifts in solids: Combined multiple pulse NMR and magic-angle spinning

    SciTech Connect

    Ryan, L.M.; Taylor, R.E.; Paff, A.J.; Gerstein, B.C.

    1980-01-01

    High-resolution nuclear magnetic resonance spectra of protons in rigid, randomly oriented solids have been measured using combined homonuclear dipolar decoupling (via multiple pulse techniques) and attenuation of chemical shift anisotropies (via magic-angle sample spinning). Under those conditions, isotropic proton chemical shifts were recorded for a variety of chemical species, with individual linewidths varying from about 55 to 110 Hz (1--2 ppm). Residual line broadening was due predominately to (i) magnetic-field instability and inhomogeneity, (ii) unresolved proton--proton spin couplings, (iii) chemical shift dispersion, (iv) residual dipolar broadening, and (v) lifetime broadening under the multiple pulse sequences used. The magnitudes of those effects and the current limits of resolution for this experiment in our spectrometer have been investigated. The compounds studied included organic solids (4, 4'-dimethylbenzophenone, 2, 6-dimethylbenzoic acid, and aspirin), polymers (polystyrene and polymethylmethacrylate), and the vitrain portion of a bituminous coal.

  12. Proton Fingerprints Portray Molecular Structures: Enhanced Description of the 1H NMR Spectra of Small Molecules

    PubMed Central

    Napolitano, José G.; Lankin, David C.; McAlpine, James B.; Niemitz, Matthias; Korhonen, Samuli-Petrus; Chen, Shao-Nong; Pauli, Guido F.

    2013-01-01

    The characteristic signals observed in NMR spectra encode essential information on the structure of small molecules. However, extracting all of this information from complex signal patterns is not trivial. This report demonstrates how computer-aided spectral analysis enables the complete interpretation of 1D 1H NMR data. The effectiveness of this approach is illustrated with a set of organic molecules, for which replicas of their 1H NMR spectra were generated. The potential impact of this methodology on organic chemistry research is discussed. PMID:24007197

  13. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoacetica metabolic profiles.

    PubMed

    Xue, Junfeng; Isern, Nancy G; Ewing, R James; Liyu, Andrei V; Sears, Jesse A; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R; Ahring, Birgitte K; Majors, Paul D

    2014-10-01

    An in situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution NMR (HR-NMR) spectroscopy. In situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at 500 MHz, and aliquots of the bioreactor contents were taken for 600-MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol, and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in situ NMR bioreactor facilitated monitoring of the fermentation process, enabling identification of intermediate and endpoint metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts. PMID:24946863

  14. Communication: Proton NMR dipolar-correlation effect as a method for investigating segmental diffusion in polymer melts.

    PubMed

    Lozovoi, A; Mattea, C; Herrmann, A; Rössler, E A; Stapf, S; Fatkullin, N

    2016-06-28

    A simple and fast method for the investigation of segmental diffusion in high molar mass polymer melts is presented. The method is based on a special function, called proton dipolar-correlation build-up function, which is constructed from Hahn Echo signals measured at times t and t/2. The initial rise of this function contains additive contributions from both inter- and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution depends on the relative mean squared displacements (MSDs) of polymer segments from different macromolecules, while the intramolecular part reflects segmental reorientations. Separation of both contributions via isotope dilution provides access to segmental displacements in polymer melts at millisecond range, which is hardly accessible by other methods. The feasibility of the method is illustrated by investigating protonated and deuterated polybutadiene melts with molecular mass 196 000 g/mol at different temperatures. The observed exponent of the power law of the segmental MSD is close to 0.32 ± 0.03 at times when the root MSD is in between 45 Å and 75 Å, and the intermolecular proton dipole-dipole contribution to the total proton Hahn Echo NMR signal is larger than 50% and increases with time. PMID:27369489

  15. Communication: Proton NMR dipolar-correlation effect as a method for investigating segmental diffusion in polymer melts

    NASA Astrophysics Data System (ADS)

    Lozovoi, A.; Mattea, C.; Herrmann, A.; Rössler, E. A.; Stapf, S.; Fatkullin, N.

    2016-06-01

    A simple and fast method for the investigation of segmental diffusion in high molar mass polymer melts is presented. The method is based on a special function, called proton dipolar-correlation build-up function, which is constructed from Hahn Echo signals measured at times t and t/2. The initial rise of this function contains additive contributions from both inter- and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution depends on the relative mean squared displacements (MSDs) of polymer segments from different macromolecules, while the intramolecular part reflects segmental reorientations. Separation of both contributions via isotope dilution provides access to segmental displacements in polymer melts at millisecond range, which is hardly accessible by other methods. The feasibility of the method is illustrated by investigating protonated and deuterated polybutadiene melts with molecular mass 196 000 g/mol at different temperatures. The observed exponent of the power law of the segmental MSD is close to 0.32 ± 0.03 at times when the root MSD is in between 45 Å and 75 Å, and the intermolecular proton dipole-dipole contribution to the total proton Hahn Echo NMR signal is larger than 50% and increases with time.

  16. Coupling effect on the proton optics from the electron lenses

    SciTech Connect

    Luo, Y.; Gu, X.; Fischer, W.

    2010-08-01

    In this note we calculate the effect of the electron lense solenoids on the proton optics. Electron lenses (e-lenses) are to be used for head-on beam-beam compensation in the Relativistic Heavy Ion Collider (RHIC). Electron lenses are to be used for head-on beam-beam compensation in the polarized proton (pp) runs to compensate the large tune spread generated by the head-on proton-proton beam-beam interactions at IP6 and IP8 in the Relativistic Heavy Ion Collider (RHIC). The main part of an electron lens is a superconducting solenoid with a longitudinal magnetic field up to 6 T. In this report, we will estimate the e-elenses effects on the {beta} and dispersion functions with 100 GeV and 250 GeV pp run lattices. Table 1 lists some lattice and beam parameters to be used in the following study.

  17. The Synthesis and Proton NMR Spectrum of Methyl 7-Cycloheptatrienylacetate: An Advanced Undergraduate Laboratory Experiment.

    ERIC Educational Resources Information Center

    Jurch, G. R., Jr.; And Others

    1980-01-01

    Describes an advanced undergraduate laboratory experiment designed to give the senior chemistry student an opportunity to apply several synthetic and purification techniques as well as possibilities for the application of NMR spectroscopy. (CS)

  18. Guanidinoacetate methyltransferase (GAMT) deficiency diagnosed by proton NMR spectroscopy of body fluids.

    PubMed

    Engelke, Udo F H; Tassini, Maria; Hayek, Joseph; de Vries, Maaike; Bilos, Appie; Vivi, Antonio; Valensin, Gianni; Buoni, Sabrina; Zannolli, Raffaella; Brussel, Wim; Kremer, Berry; Salomons, Gajja S; Veendrick-Meekes, Monique J B M; Kluijtmans, Leo A J; Morava, Eva; Wevers, Ron A

    2009-06-01

    In patients with guanidinoacetate methyltransferase (GAMT) deficiency several parameters may point towards the diagnosis of GAMT deficiency. These include the low levels of creatine and creatinine in urine, the high concentration of guanidinoacetic acid (GAA) in urine and the low levels of creatine and creatinine in the cerebrospinal fluid (CSF). In this study, body fluids from 10 GAMT deficient patients were analysed using (1)H NMR spectroscopy. The urine 1D (1)H NMR spectra of all the patients showed a doublet resonance at 3.98 ppm (pH 2.50) derived from GAA present in high concentration. For this compound, a good recovery and good correlation was found between an LC-MS/MS method and (1)H NMR spectroscopy. In CSF NMR spectra of these patients, the singlet resonances of creatine and creatinine (3.05 and 3.13 ppm, respectively) were absent (normally always present in (1)H NMR spectra of CSF). Due to overlap by other resonances, the doublet of GAA could not be observed. Our data demonstrate that (1)H NMR spectroscopy of urine and CSF can be used to diagnose patients with GAMT deficiency. PMID:19288536

  19. Interactions of hydrogen with alkali promoted Ru/SiO{sub 2} catalysts: A proton NMR study

    SciTech Connect

    Ozbay, U.D.

    1994-05-10

    Role of H spillover to the silica support was studied using chemisorption; a strongly bound component of spilled over H was found in the silica support which interfered with accurate measurements of active metal sites via volumetric strong H chemisorption. The volumetric chemisorption technique was modified so that measurement times were reduced from 12--36 h to 1 h. The active Ru surface was characterized means of changes in proton spin counts and NMR Knight shifts vs alkali loading. Na, K blocked the active surface of Ru metal, but Cs was pushed off by H chemisorption. The alkali promoters restricted H mobility on both metal surface and at the metal support interfaces; this is consistent with effects on Fischer-Tropsch synthesis. {sup 1}H NMR was used to study the effect of the active metal and promoter on support hydroxyl groups. The OH group density in the silica support decreased with metal and/or promoter loading, but not on a one-to-one basis; the exchange efficiency of the hydroxyls decreased with atomic size of the alkali metal. An additional downfield proton resonance was detected which was assigned to the alkali hydroxide species in the support.

  20. Transient characteristics for proton gating in laterally coupled indium-zinc-oxide transistors.

    PubMed

    Liu, Ning; Zhu, Li Qiang; Xiao, Hui; Wan, Chang Jin; Liu, Yang Hui; Chao, Jin Yu

    2015-03-25

    The control and detection over processing, transport and delivery of chemical species is of great importance in sensors and biological systems. The transient characteristics of the migration of chemical species reflect the basic properties in the processings of chemical species. Here, we observed the field-configurable proton effects in a laterally coupled transistor gated by phosphorosilicate glass (PSG). The bias on the lateral gate would modulate the interplay between protons and electrons at the PSG/indium-zinc-oxide (IZO) channel interface. Due to the modulation of protons flux within the PSG films, the IZO channel current would be modified correspondingly. The characteristic time for the proton gating is estimated to be on the order of 20 ms. Such laterally coupled oxide based transistors with proton gating are promising for low-cost portable biosensors and neuromorphic system applications. PMID:25741771

  1. Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

  2. Analysis of Chain Branch of Polyolefins by a New Proton NMR Approach.

    PubMed

    Jung, Minhwan; Lee, Yura; Kwak, Sooyoung; Park, Heeyong; Kim, Byoungsoo; Kim, Sulhee; Lee, Kwang Hwan; Cho, Hye Sung; Hwang, Kwang Yeon

    2016-02-01

    The crystallinity of polyethylene, which significantly affects the properties of the polymer, is quite sensitive to the concentration of its branches. Thus, it is necessary to estimate branch concentration with reasonable accuracy. Currently, (13)C NMR and gel permeation chromatography-Fourier transform infrared spectroscopy are widely-used analysis methods for the analysis of branch concentration. Despite several advantages, these methods sometimes have limitations. For instance, the preparation of samples for (13)C- NMR is tedious because high-concentration samples are required and the time for analysis is greater than 12 h. To more efficiently estimate the branch concentration of polyethylene, we developed a new high-field (1)H NMR method with an improved peak resolution by employing (1) homonuclear decoupling and (2) 2D heteronuclear correlation. The new method was observed to significantly reduce the experimental time to ∼ 30 min; furthermore, sample preparation was relatively simple because the method did not require high-concentration samples. PMID:26713895

  3. High-Affinity Proton Donors Promote Proton-Coupled Electron Transfer by Samarium Diiodide.

    PubMed

    Chciuk, Tesia V; Anderson, William R; Flowers, Robert A

    2016-05-10

    The relationship between proton-donor affinity for Sm(II) ions and the reduction of two substrates (anthracene and benzyl chloride) was examined. A combination of spectroscopic, thermochemical, and kinetic studies show that only those proton donors that coordinate or chelate strongly to Sm(II) promote anthracene reduction through a PCET process. These studies demonstrate that the combination of Sm(II) ions and water does not provide a unique reagent system for formal hydrogen atom transfer to substrates. PMID:27061351

  4. Proton and carbon NMR measurements of the effects of hydration on the wheat protein ω-gliadin

    NASA Astrophysics Data System (ADS)

    Belton, P. S.; Gil, A. M.; Grant, A.; Alberti, E.; Tatham, A. S.

    1998-07-01

    The wheat protein ω-gliadin consists of a simple repeat sequence composed mainly of proline and glutamine. It thus represents a simple model for many cereal proteins and other proline and glutamine rich sequences which occur in multiple repeats. The behaviour on hydration has been examined by the measurement of proton NMR relaxation times. Sidechain motions (methyl and amino group rotation, proline ring puckering) were largely responsible for T1 relaxation. It was found that the glass transition does not affect T1 and T1 ρ relaxation and only affects transverse relaxation. Magic angle spinning experiments have been used to observe line narrowed proton spectra as well as carbon cross polarisation spectra. In the proton spectra, at high levels of hydration, backbone and sidechain NH groups are observed indicating that whole segments of the protein chain are in the mobile regime. The carbon spectra are characterised by a loss of the proline C δ signal intensity at high levels of hydration indicating the involvement of proline in the hydration process. It is concluded that the behaviour of ω-gliadin on hydration may be explained by the formation of mobile protein loops together with residual regions of strong interprotein interaction.

  5. Prospective Real Time Head Motion Correction Using Inductively Coupled Wireless NMR Probes

    PubMed Central

    Sengupta, Saikat; Tadanki, Sasidhar; Gore, John C.; Welch, E. Brian

    2014-01-01

    Purpose Head motion continues to be a major source of artifacts and data quality degradation in MRI. The goal of this work was to develop and demonstrate a novel technique for prospective, 6 degrees of freedom (6DOF) rigid body motion estimation and real time motion correction using inductively coupled wireless nuclear magnetic resonance (NMR) probe markers. Methods Three wireless probes that are inductively coupled with the scanner’s RF setup serve as fiducials on the subject’s head. A 12 ms linear navigator module is interleaved with the imaging sequence for head position estimation, and scan geometry is updated in real time for motion compensation. Flip angle amplification in the markers allows the use of extremely small navigator flip angles (~1°). A novel algorithm is presented to identify marker positions in the absence of marker specific receive channels. The method is demonstrated for motion correction in 1 mm3 gradient recalled echo experiments in phantoms and humans. Results Significant improvement of image quality is demonstrated in phantoms and human volunteers under different motion conditions. Conclusion A novel real time 6 DOF head motion correction technique based on wireless NMR probes is demonstrated in high resolution imaging at 7 Tesla. PMID:24243810

  6. Visualizing the kinetic power stroke that drives proton-coupled Zn(II) transport

    PubMed Central

    Gupta, Sayan; Chai, Jin; Cheng, Jie; D'Mello, Rhijuta; Chance, Mark R.; Fu, Dax

    2014-01-01

    The proton gradient is a principal energy source for respiration-dependent active transport, but the structural mechanisms of proton-coupled transport processes are poorly understood. YiiP is a proton-coupled zinc transporter found in the cytoplasmic membrane of E. coli, and the transport-site of YiiP receives protons from water molecules that gain access to its hydrophobic environment and transduces the energy of an inward proton gradient to drive Zn(II) efflux1,2. This membrane protein is a well characterized member3-7 of the protein family of cation diffusion facilitators (CDFs) that occurs at all phylogenetic levels8-10. X-ray mediated hydroxyl radical labeling of YiiP and mass spectrometric analysis showed that Zn(II) binding triggered a highly localized, all-or-none change of water accessibility to the transport-site and an adjacent hydrophobic gate. Millisecond time-resolved dynamics revealed a concerted and reciprocal pattern of accessibility changes along a transmembrane helix, suggesting a rigid-body helical reorientation linked to Zn(II) binding that triggers the closing of the hydrophobic gate. The gated water access to the transport-site enables a stationary proton gradient to facilitate the conversion of zinc binding energy to the kinetic power stroke of a vectorial zinc transport. The kinetic details provide energetic insights into a proton-coupled active transport reaction. PMID:25043033

  7. Role of pendant proton relays and proton-coupled electron transfer on the hydrogen evolution reaction by nickel hangman porphyrins

    PubMed Central

    Bediako, D. Kwabena; Solis, Brian H.; Dogutan, Dilek K.; Roubelakis, Manolis M.; Maher, Andrew G.; Lee, Chang Hoon; Chambers, Matthew B.; Hammes-Schiffer, Sharon; Nocera, Daniel G.

    2014-01-01

    The hangman motif provides mechanistic insights into the role of pendant proton relays in governing proton-coupled electron transfer (PCET) involved in the hydrogen evolution reaction (HER). We now show improved HER activity of Ni compared with Co hangman porphyrins. Cyclic voltammogram data and simulations, together with computational studies using density functional theory, implicate a shift in electrokinetic zone between Co and Ni hangman porphyrins due to a change in the PCET mechanism. Unlike the Co hangman porphyrin, the Ni hangman porphyrin does not require reduction to the formally metal(0) species before protonation by weak acids in acetonitrile. We conclude that protonation likely occurs at the Ni(I) state followed by reduction, in a stepwise proton transfer–electron transfer pathway. Spectroelectrochemical and computational studies reveal that upon reduction of the Ni(II) compound, the first electron is transferred to a metal-based orbital, whereas the second electron is transferred to a molecular orbital on the porphyrin ring. PMID:25298534

  8. Biosynthesis and NMR analysis of a 73-residue domain of a Saccharomyces cerevisiae G protein-coupled receptor.

    PubMed

    Estephan, Racha; Englander, Jacqueline; Arshava, Boris; Samples, Karen L; Becker, Jeffrey M; Naider, Fred

    2005-09-01

    The yeast Saccharomyces cerevisiae alpha-factor pheromone receptor (Ste2p) was used as a model G protein-coupled receptor (GPCR). A 73-mer multidomain fragment of Ste2p (residues 267-339) containing the third extracellular loop, the seventh transmembrane domain, and 40 residues of the cytosolic tail (E3-M7-24-T40) was biosynthesized fused to a carrier protein. The multidomain fusion protein (designated M7FP) was purified to near homogeneity as judged by HPLC and characterized by mass spectrometry. In minimal medium, 30-40 mg of M7FP were obtained per liter of culture. The 73-residue peptide was released from its carrier by CNBr and obtained in wild-type, (15)N, and (13)C/(15)N forms. The E3-M7-24-T40 peptide integrated into 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] and dodecylphosphocholine micelles at concentrations (200-500 microM) suitable for NMR investigations. HSQC experiments performed in organic solvents and detergent micelles on (15)N-labeled E3-M7-24-T40 showed a clear dispersion of the nitrogen-amide proton correlation cross-peaks indicative of a pure, uniformly labeled molecule that assumed a partially ordered structure. NOE connectivities, chemical shift indices, J-coupling analysis, and structural modeling suggested that in trifluoroethanol/water (1:1) helical subdomains existed in both the transmembrane and cytoslic tail of the multidomain peptide. Similar conclusions were reached in chloroform/methanol/water (4:4:1). As the cytosolic tail participates in down-regulation of Ste2p, the helical regions in the Ste2p tail may play a role in protein-protein interactions involved in endocytosis. PMID:16128581

  9. Kohn-Sham calculations of NMR shifts for paramagnetic 3d metal complexes: protocols, delocalization error, and the curious amide proton shifts of a high-spin iron(ii) macrocycle complex.

    PubMed

    Martin, Bob; Autschbach, Jochen

    2016-08-01

    A theory for the nuclear chemical shifts of molecules in arbitrary spin states is applied to a set of paramagnetic organometallic complexes of 3d metals. Ligand chemical shifts are calculated and analyzed using Kohn-Sham (KS) density functional theory with and without relativistic corrections. The roles of the KS delocalization error, Gaussian-type versus Slater-type basis sets, relativistic effects (scalar and spin-orbit), and zero field splitting (ZFS) are investigated. A strong functional dependence of the chemical shifts is apparent and correlated with the delocalization error. The functional dependence is between one and two orders of magnitude larger than variations of the NMR shifts due the other influences that are investigated. ZFS effects are negligible in the determination of the NMR chemical shifts of the complexes except at very low temperatures. The DFT calculated shifts agree reasonably well with experiment. A 73 ppm difference in the NMR shifts of the two protons in the amide groups of a high-spin Fe(ii) macrocycle complex arises from selective O → Fe dative bonding that only involves the transfer of β spin density, along with orbital delocalization throughout the ligand bonding framework which electronically couples the coordinating oxygen lone pair orbitals directly to the amide trans proton. PMID:26952694

  10. Mechanism of proton-coupled quinone reduction in Photosystem II

    PubMed Central

    Saito, Keisuke; Rutherford, A. William; Ishikita, Hiroshi

    2013-01-01

    Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, QA and QB, working in series. QA is a one-electron carrier, whereas QB undergoes sequential reduction and protonation to form QBH2. QBH2 exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to QB•– occurs from the protonated, D1-His252 to QB•– via D1-Ser264. The second PT is likely to occur from D1-His215 to QBH− via an H-bond with an energy profile with a single well, resulting in the formation of QBH2 and the D1-His215 anion. The pathway for reprotonation of D1-His215– may involve bicarbonate, D1-Tyr246 and water in the QB site. Formate ligation to Fe2+ did not significantly affect the protonation of reduced QB, suggesting that formate inhibits QBH2 release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe3+ state in the presence of QB•–, a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for QB reduction is presented. PMID:23277574

  11. Mechanism of proton-coupled quinone reduction in Photosystem II.

    PubMed

    Saito, Keisuke; Rutherford, A William; Ishikita, Hiroshi

    2013-01-15

    Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, Q(A) and Q(B), working in series. Q(A) is a one-electron carrier, whereas Q(B) undergoes sequential reduction and protonation to form Q(B)H(2). Q(B)H(2) exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to Q(B)(•-) occurs from the protonated, D1-His252 to Q(B)(•)(-) via D1-Ser264. The second PT is likely to occur from D1-His215 to Q(B)H(-) via an H-bond with an energy profile with a single well, resulting in the formation of Q(B)H(2) and the D1-His215 anion. The pathway for reprotonation of D1-His215(-) may involve bicarbonate, D1-Tyr246 and water in the Q(B) site. Formate ligation to Fe(2+) did not significantly affect the protonation of reduced Q(B), suggesting that formate inhibits Q(B)H(2) release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe(3+) state in the presence of Q(B)(•-), a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for Q(B) reduction is presented. PMID:23277574

  12. Spin asymmetries for elastic proton scattering and the spin-dependent couplings of the Pomeron

    SciTech Connect

    Trueman, T. L.

    2008-03-01

    This paper serves as a report on the large amount of analysis done in conjunction with the polarized proton program at the Relavitistic Heavy Ion Collider at Brookhaven National Laboratory. This comprises elastic scattering data of protons on protons in colliding beam or fixed target mode and proton beams on carbon targets. In addition to providing a model for the energy dependence of the analyzing power of elastic scattering needed for proton polarimetry, it also provides some significant information about the spin dependence of dominant Regge poles. Most notably, the data indicate that the Pomeron has a significant spin-flip coupling. This allows the exploration of the double-spin flip asymmetry A{sub NN} for which some data over a wide energy range are now available, along with a concrete realization of a proposed Odderon search.

  13. NMR J-coupling constants in cisplatin derivatives studied by molecular dynamics and relativistic DFT.

    PubMed

    Sutter, Kiplangat; Truflandier, Lionel A; Autschbach, Jochen

    2011-06-01

    Solvent effects on J((195)Pt-(15)N) one-bond nuclear spin-spin coupling constants (J(PtN)) of cisplatin [cis-diamminedichloroplatinum(II)] and three cisplatin derivatives are investigated using a combination of density functional theory (DFT) based ab initio molecular dynamics (aiMD) and all-electron relativistic DFT NMR calculations employing the two-component relativistic zeroth-order regular approximation (ZORA). Good agreement with experiment is obtained when explicit solvent molecules are considered and when the computations are performed with a hybrid functional. Spin-orbit coupling causes only small effects on J(PtN) . Key factors contributing to the magnitude of coupling constants are elucidated, with the most significant being the presence of solvent as well as the quality of the density functional and basis set combination. The solvent effects are of the same magnitude as J(PtN) calculated for gas-phase geometries. However, the trends of J(PtN) among the complexes are already present in the gas phase. Results obtained with a continuum solvent model agree quite well with the aiMD results, provided that the Pt solvent-accessible radius is carefully chosen. The aiMD results support the existence of a partial hydrogen-bond-like inverse-hydration-type interaction affording a weak (1)J(Pt⋅⋅⋅H(w)) coupling between the complexes and the coordinating water molecule. PMID:21381179

  14. Solid-state proton NMR of paramagnetic metal complexes: DANTE spin echoes for selective excitation in inhomogeneously broadened lines

    NASA Astrophysics Data System (ADS)

    Carnevale, Diego; Perez Linde, A. J.; Bauer, Gerald; Bodenhausen, Geoffrey

    2013-08-01

    The paramagnetic complex bis(oxazolinylphenyl)amine-Fe(III)Cl2 is investigated by means of solid-state proton NMR at 18.8 T (800 MHz) using magic-angle spinning at 65 kHz. Spin echoes that are excited and refocused by combs of rotor-synchronized pulses in the manner of 'Delays Alternating with Nutation for Tailored Excitation' (DANTE) allow one to characterize different chemical environments that severely overlap in conventional MAS spectra. Such sequences combine two apparently contradictory features: an overall bandwidth exceeding several MHz, and very selective irradiation of a few kHz within inhomogeneously broadened sidebands. The experimental hyperfine interactions correlate well with DFT calculations.

  15. Free volume of poly(perfluorosulfonic acid)/SiO 2 composite proton exchange membranes by 129Xe NMR

    NASA Astrophysics Data System (ADS)

    Utiu, Lavinia; Filipoi, Carmen; Demco, Dan E.; Zhu, Xiaomin; Vinokur, Rostislav; Conradi, Oliver; Graichen, Andreas; Blümich, Bernhard; Möller, Martin

    2011-04-01

    Poly(perfluorosulfonic acid)/silica (PFSA/SiO2) composites were investigated by 129Xe NMR spectroscopy and relaxometry. 129Xe chemical shift extrapolated to zero pressure was used for calculation of average free volume hole size. This quantity reaches a maximum at 2 wt.% SiO2 that could be correlated to the performance of composites proton exchange membrane. 129Xe longitudinal magnetization relaxation revealed a bimodal distribution of the free volume that was explained by the presence of xenon atoms in the backbone and pendant-chain domains. Thus, the free volume is heterogeneous and depends on the content of SiO2. Implications of the free volume changes for the hydrogen crossover through PFSA/SiO2 membranes are also discussed.

  16. Proton NMR study of a complex between the lac repressor headpiece and a 22 base pair symmetric lac operator

    SciTech Connect

    Lamerichs, R.M.J.N.; Boelens, R.; van der Marel, G.A.; van Boom, J.H.; Kaptein, R.; Buck, F.; Fera, B.; Rueterjans, H. )

    1989-04-04

    A complex between the lac repressor headpiece and a fully symmetric tight-binding 22 bp lac operator was studied by 2D NMR. Several 2D NOE spectra were recorded for the complex in both H{sub 2}O and {sup 2}H{sub 2}O. Many NOE cross-peaks between the headpiece and DNA could be identified, and changes in the chemical shift of the DNA protons upon complex formation were analyzed. Comparison of these data with those obtained for a complex between the headpiece and a 14 bp half-operator, studied previously, shows that two headpieces form a specific complex with the 22 bp lac operator in which each headpiece binds in the same way as found for the 14 bp complex. The orientation of the recognition helix in the major groove of DNA in these complexes is opposite with respect to the dyad axis to that found for other repressors.

  17. Proton NMR characterization of isomeric sulfmyoglobins: preparation, interconversion, reactivity patterns, and structural features

    SciTech Connect

    Chatfield, M.J.; La Mar, G.N.; Kauten, R.J.

    1987-11-03

    The preparations of sulfmyoglobin (sulf-Mb) by standard procedures have been found heterogeneous by /sup 1/H NMR spectroscopy. Presented here are the results of a comprehensive study of the factors that influence the selection among the three dominant isomeric forms of sperm whale sulf-Mb and their resulting detailed optical and /sup 1/H NMR properties as related to their detectability and structural properties of the heme pocket. A single isomer is formed initially in the deoxy state; further treatment in any desired oxidation/ligation state can yield two other major isomers. Acid catalysis and chromatography facilitate formation of a second isomer, particularly in the high-spin state. At neutral pH, a third isomer is formed by a first-order process. The processes that alter oxidation/ligation state are found to be reversible and are judged to affect only the metal center, but the three isomeric sulf-Mbs are found to exhibit significantly different ligand affinity and chemical stability. The present results allow, for the first time, a rational approach for preparing a given isomeric sulf-Mb in an optimally pure state for subsequent characterization by other techniques. While optical spectroscopy can distinguish the alkaline forms, only /sup 1/H NMR clearly distinguishes all three ferric isomers. The hyperfine shift patterns in the various oxidation/spin states of sulf-Mbs indicate relatively small structural alteration, and the proximal and distal sides of the heme suggest that peripheral electronic effects are responsible for the differentially reduced ligand affinities for the three isomeric sulf-Mbs. The first /sup 1/H NMR spectra of sulfhemoglobins are presented, which indicate a structure similar to that of the initially formed sulf-Mb isomer but also suggest the presence of a similar molecular heterogeneity as found for sulf-Mb, albiet to a smaller extent.

  18. Salt-dependent structure change and ion binding in cytochrome c studied by two-dimensional proton NMR

    SciTech Connect

    Feng, Yiqing; Englander, S.W. )

    1990-04-10

    To search for salt-dependent structure changes that might help to explain physicochemical differences observed in previous solution studies, two-dimensional proton NMR spectra of reduced and oxidized cytochrome c were recorded at relatively high and low salt concentrations. The results rule out substantial ionic strength dependent structure change in either redox form over the salt concentrations tested. Chemical shift changes were found for several residues within a limited segment of the oxidized protein, most prominently in the sequence Lys-86, Lys-87, Lys-88, Thr-89. A salt-dependent binding of phosphate anion(s) at this site, as observed earlier by others, is indicated. The binding of one or two phosphates at the cytochrome c surface can explain earlier small-angle X-ray scattering observations of an increase in the calculated radius of gyration of the oxidized protein at the same low-salt condition used here. The results obtained support the view that the absence of sizeable redox-dependent structure change observed in X-ray and NMR studies at varying salt conditions is characteristic of the protein at all salt conditions above the low millimolar range. Physicochemical differences between oxidized and reduced cytochrome c apparently represent differences in stability without patent structure change.

  19. Investigating the Dissolution Performance of Amorphous Solid Dispersions Using Magnetic Resonance Imaging and Proton NMR.

    PubMed

    Tres, Francesco; Coombes, Steven R; Phillips, Andrew R; Hughes, Leslie P; Wren, Stephen A C; Aylott, Jonathan W; Burley, Jonathan C

    2015-01-01

    We have investigated the dissolution performance of amorphous solid dispersions of poorly water-soluble bicalutamide in a Kollidon VA64 polymeric matrix as a function of the drug loading (5% vs. 30% bicalutamide). A combined suite of state-of-the-art analytical techniques were employed to obtain a clear picture of the drug release, including an integrated magnetic resonance imaging UV-Vis flow cell system and 1H-NMR. Off-line 1H-NMR was used for the first time to simultaneously measure the dissolution profiles and rates of both the drug and the polymer from a solid dispersion. MRI and 1H-NMR data showed that the 5% drug loading compact erodes linearly, and that bicalutamide and Kollidon VA64 are released at approximately the same rate from the molecular dispersion. For the 30% extrudate, data indicated a slower water ingress into the compact which corresponds to a slower dissolution rate of both bicalutamide and Kollidon VA64. PMID:26378506

  20. Proton nuclear magnetic resonance spectroscopy (NMR) methods for determining the purity of reference drug standards and illicit forensic drug seizures.

    PubMed

    Hays, Patrick A

    2005-11-01

    A rapid, sensitive, accurate, precise, reproducible, and versatile method for determining the purity of reference drug standards and the routine analysis of illicit drugs and adulterants using proton (1H) Nuclear Magnetic Resonance (NMR) Spectroscopy is presented. The methodology uses a weighed sample dissolved in a deuterated solvent or solvent mixture containing a high purity internal standard. The NMR experiment employs 8 scans using a 45 second delay and 90 degrees pulse. In the determination of purity of reference standards, the number of quantitative determinations available is equal to the number of peak groups that are baseline resolved. The relative standard deviation (RSD) of these signals is usually < 1% for pure standards, and the results agree well with other purity determining methods. This method can also aid in the determination of correct molecular weight for standards containing an unknown number of waters of hydration or an unknown number of acids per drug in salts. Because the molar response for the hydrogen nucleus is 1 for all compounds, and since no separation media are used, only one linearity study is required to test a probe. In the presented study, the linearity of the NMR probe was determined using methamphetamine HCl dissolved in deuterium oxide (D2O) with maleic acid as the internal standard (5 mg) for a range of concentrations from 0.033 to 69.18 mg/ml with a resulting correlation coefficient of >0.9999 for all 6 methamphetamine peak groups. The spectra of complex illicit heroin, methamphetamine, MDMA, and cocaine samples are presented, as well as an extensive list of compounds, their solubilities and the solvent(s) and internal standard used. PMID:16382828

  1. Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE

    PubMed Central

    Wisedchaisri, Goragot; Park, Min-Sun; Iadanza, Matthew G.; Zheng, Hongjin; Gonen, Tamir

    2014-01-01

    The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. PMID:25088546

  2. Proton and tritium NMR relaxation studies of peptide inhibitor binding to bacterial collagenase: Conformation and dynamics

    SciTech Connect

    Dive, V.; Lai, A.; Valensin, G.; Saba, G.; Yiotakis, A.; Toma, F. )

    1991-02-15

    The interaction of succinyl-Pro-Ala, a competitive inhibitor of Achromobacter iophagus collagenase, with the enzyme was studied by longitudinal proton and tritium relaxation. Specific deuterium and tritium labeling of the succinyl part at vicinal positions allowed the measurement of the cross-relaxation rates of individual proton or tritium spin pairs in the inhibitor-enzyme complex as well as in the free inhibitor. Overall correlation times, internuclear distances, and qualitative information on the internal mobility in Suc1 (as provided by the generalized order parameter S2) could be deduced by the comparison of proton and tritium cross-relaxation of spin pairs at complementary positions in the -CH2- CH2- moiety as analyzed in terms of the model-free approach by Lipari and Szabo. The conformational and motional parameters of the inhibitor in the free and enzyme-bound state were directly compared by this method. The measurement of proton cross-relaxation in the Ala residue provided additional information on the inhibitor binding. The determination of the order parameter in different parts of the inhibitor molecule in the bound state indicates that the succinyl and alanyl residues are primarily involved in the interaction with the enzyme activity site. The succinyl moiety, characterized in solution by the conformational equilibrium among the three staggered rotamers--i.e., trans: 50%; g+: 20%; g-: 30%--adopted in the bound state the unique trans conformation.

  3. Orientational landscapes of peptides in membranes: prediction of (2)H NMR couplings in a dynamic context.

    PubMed

    Esteban-Martín, Santi; Giménez, Diana; Fuertes, Gustavo; Salgado, Jesús

    2009-12-01

    Unlike soluble proteins, membrane polypeptides face an anisotropic milieu. This imposes restraints on their orientation and provides a reference that makes structure prediction tractable by minimalistic thermodynamic models. Here we use this framework to build orientational distributions of monomeric membrane-bound peptides and to predict their expected solid-state (2)H NMR quadrupolar couplings when labeled at specific side chain positions. Using a complete rigid-body sampling of configurations relative to an implicit lipid membrane, peptide free energy landscapes are calculated. This allows us to obtain probability distributions of the peptide tilt, azimuthal rotation, and depth of membrane insertion. The orientational distributions are broad and originate from an interplay among the three relevant rigid-body degrees of freedom, which allows population of multiple states in shallow free energy minima. Remarkably, only when the orientational distributions are taken into account do we obtain a close correlation between predicted (2)H NMR splittings and values measured in experiments. Such a good correlation is not seen with splittings calculated from single configurations, being either the averaged or the lowest free energy state, showing there are distributions, rather than single structures, that best define the peptide-membrane systems. Moreover, we propose that these distributions contribute to the understanding of the rigid-body dynamics of the system. PMID:19860438

  4. Cross polarization and magic angle sample spinning NMR spectra of model organic compounds. 1. Highly protonated molecules

    SciTech Connect

    Alemany, L.B.; Grant, D.M.; Pugmire, R.J.; Alger, T.D.; Zilm, K.W.

    1983-04-20

    CP/MAS /sup 13/C NMR spectra were obtained at various contact times on ten solid organic compounds containing a variety of simple functional groups. The spectra show that signal intensities that agree with atomic ratios can be obtained with a contact time of 2.25 ms and often with a contact time as short as about 1 ms. Computer analysis of signal intensities obtained at a minimum of ten different contact times provides T/sub CH/ data that are consistent with these experimental results. The experimental results are also consistent with the previously reported lack of significant variation in the spectra of complex organic solids obtained with contact times of about 1 to 3 ms. In general, nonprotonated carbon atoms polarize more slowly than protonated carbon atoms. The compounds exhibit a wide range of proton spin lattice relaxation times. Some compounds exhibit more resonances than are found in the /sup 13/C(/sup 1/H) spectra of the compounds in solution because the crystalline environment removes the nominal spatial equivalence found for carbon atoms related to each other by unimolecular symmetry elements.

  5. Proton Dynamics on Goethite Nanoparticles and Coupling to Electron Transport.

    PubMed

    Zarzycki, Piotr; Smith, Dayle M; Rosso, Kevin M

    2015-04-14

    The surface chemistry of metal oxide particles is governed by the charge that develops at the interface with aqueous solution. Mineral transformation, biogeochemical reactions, remediation, and sorption dynamics are profoundly affected in response. Here we report implementation of replica-exchange constant-pH molecular dynamics simulations that use classical molecular dynamics for exploring configurational space and Metropolis Monte Carlo walking through protonation space with a simulated annealing escape route from metastable configurations. By examining the archetypal metal oxide, goethite (α-FeOOH), we find that electrostatic potential gradients spontaneously arise between intersecting low-index crystal faces and across explicitly treated oxide nanoparticles at a magnitude exceeding the Johnson-Nyquist voltage fluctuation. Fluctuations in adsorbed proton density continuously repolarize the surface potential bias between edge-sharing crystal faces, at a rate slower than the reported electron-polaron hopping rate in goethite interiors. This suggests that these spontaneous surface potential fluctuations will control the net movement of charge carriers in the lattice. PMID:26574382

  6. Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings.

    PubMed

    Ruan, Ke; Tolman, Joel R

    2005-11-01

    The measurement of independent sets of NMR residual dipolar couplings (RDCs) in multiple alignment media can provide a detailed view of biomolecular structure and dynamics, yet remains experimentally challenging. It is demonstrated here that independent sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a strained polyacrylamide gel matrix. Using this composite medium, molecular alignment can be modulated by varying the angle between the directors of ordering for the Pf1 and strained gel matrix, or by varying the ionic strength or concentration of the Pf1 particles. This approach offers significant advantages in that greater experimental control can be exercised over the acquisition of multi-alignment RDC data while a homogeneous chemical environment is maintained across all of the measured RDC data. PMID:16248635

  7. Coupled effect of salt and pH on proteins probed with NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kukic, Predrag; O'Meara, Fergal; Hewage, Chandralal; Erik Nielsen, Jens

    2013-07-01

    The coupled effect of ionic strength (50-400 mM) and pH (2-8) on ionization and conformation equilibria of lysozyme was studied using NMR spectroscopy. Observed changes in pKa values of the ionizable groups were found to originate from perturbations in the geometry of hydrogen bonds rather than screening of electric fields. Moreover, at the ionic strengths used here, salt-induced local conformational changes had a dominant effect on chemical shifts measured on 1HN and 15N amide nuclei. Accurate modeling of these localized perturbations in structure-based energy calculations is a necessary prerequisite on the way to complete understanding of any salt-induced processes in proteins.

  8. Studies of Zinc Oxide Nanocrystals: Quantification of Capping Ligands and the Coupling of Protons and Electrons

    NASA Astrophysics Data System (ADS)

    Valdez, Carolyn N.

    The energetics of semiconductors are widely relevant to technologies ranging from chemical- and photo-catalysis to charge injection in photovoltaic materials. In these processes involving electron transfer, protons often play a critical but overlooked role in facilitating charge transfer. For example, the conduction band energies of most metal oxides in contact with an aqueous solution demonstrate a Nernstian pH dependence, an observation that cannot be explained by surface protonation models. Given that a Nernstian dependence is typically attributed to proton coupled electron transfer (PCET), we are interested in determining if the reduction of metal oxides can also be described by PCET. Zinc oxide (ZnO) nanocrystals (NCs) were chosen as a model system given the broad range of previous research on bulk and nanocrystalline forms of ZnO, the relative ease of synthesis and characterization, and their use in developing a fundamental understanding of interfacial electron transfer. We demonstrate that photochemically reduced NCs react with hydrogen-atom acceptors, indicating that both electrons and protons are transferred by the NCs. To isolate the influence of a proton coupled to the extra electron in the conduction band, the NCs have also been reduced chemically. Addition of an excess of the one-electron reductant CoCp*2 (Cp* = pentamethylcyclopentadienyl, -1.94 V vs. Fc/Fc+) gives NCs that contain extra electrons in the conduction band, without protons that arise from photoreduction. Protons can also be individually added stoichiometrically to the NCs by either a photoreduction/oxidation sequence or by addition of acid. Using these methods, we have shown that the presence of one extra proton drastically alters the redox potential of the NCs. With the addition of acid the NC orbitals are lowered, allowing the systematic variation of driving force for electron transfer from the reductant to the NCs. In the presence of excess reductant and acid, the number of electrons

  9. Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

    SciTech Connect

    Qu, Yi; Feng, Ju; Deng, Shuang; Cao, Li; Zhang, Qibin; Zhao, Rui; Zhang, Zhaorui; Jiang, Yuxuan; Zink, Erika M.; Baker, Scott E.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Hu, Jian Z.; Wu, Si

    2014-11-19

    Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.

  10. Complex dynamics of 1.3.5-trimethylbenzene-2.4.6-D3 studied by proton spin-lattice NMR relaxation and second moment of NMR line

    NASA Astrophysics Data System (ADS)

    Hołderna-Natkaniec, K.; Latanowicz, L.; Medycki, W.; Świergiel, J.; Natkaniec, I.

    2015-02-01

    Molecular dynamics of a solid 1.3.5-trimethylbenzene-2.4.6-D3 in phase I is studied on the basis of the proton T1 (24.7 MHz and 15 MHz) relaxation time measurements and the proton second moment of NMR line, M2. The measurements of the T1 were performed for temperatures from 20 to 167 K, while those of the second moment M2 from 23 to 220 K. The phase I was accurately prepared. The obtained second moment, M2 values were correlated with those based on T1 relaxation time measurements. The proton spin pairs of the methyl groups perform a complex motion being a resultant of two components characterized by the correlation times τ3T and τ3H, referring to the tunneling and over the barrier jumps in a triple potential. For τ3H the Arrhenius temperature dependence was assumed, while for τ3T - the Schrödinger one. The jumps over the barrier causes a minimum in T1 (24.7 MHz) at temperature about 35 K. The high temperatures slope of this minimum permits evaluation of the activation energy as EH=2.0 kJ/mol. The relaxation time T1 is temperature independent in the lowest temperature regime. This indicates that tunnelling correlation time assumes a constant value of about 1.3·10-10 s according to the Schrödinger equation (τ3T ≈ τ03T e B√{EH } at lowest temperatures). The tunneling jumps of methyl protons reduce M2 from the rigid lattice value 22.6 G2 to the value 5.7 G2 at zero Kelvin temperature. The second reduction to the value 1.41 G2 at 4.5-7 K is due to C3 jumps over the barrier. According to the Schrödinger equation the tunnelling jumps ceases above Ttun temperature where the thermal energy is equal to the activation energy. The Ttun equals 43.8 K (from T1 data fit, EH=2.0 kJ/mol) or 35 K (from M2 data fit, EH=1.47 kJ/mol). The second moment assumes again the value 5.7 G2 above Ttun temperature. The tunneling splitting, ωT, was estimated equal 2.47 GHz as best fit parameter from the T1 fit. The symmetrical T1 minimum indicates the same value of ωT for the all

  11. Proton NMR spectral study of UV treated live Escherichia coli Bacteria

    NASA Astrophysics Data System (ADS)

    Sorokopud, Michael

    The lethal effects of ultraviolet radiation on microorganisms have been known and utilized for many years. In sufficiently high photon fluences, light and in particular, UV light, is an effective and subtle means of killing or at least immobilizing most, if not all cells and micro-organisms. Because of their small size, light can penetrate the enclosing protective walls and enter the inner volumes where it can break organic bonds in components that are vital to cell function. Despite the fact that a very low dose of UV light (1-9 mJ/cm2) has been shown to inactivate many micro-organisms, there remains a dearth of biological information about light induced effects in molecules and their interactions within living microbial systems. The use of 1H NMR as a spectroscopic tool was chosen to undertake an examination of the possible effects resulting from exposing E. coli to lethal fluencies of UV radiation. Once sample preparation, treatment, and NMR mounting methods were optimized, the high sensitivity and high resolution capabilities of the method produced reproducible results for a series of experiments. These results reveal significant changes in the ratio of the 1H NMR spectra of the treated to untreated E.coli samples when the treated sample was exposed to a lethal fluence of 275nm light. Photons at the 275nm wavelength, used in this study, have enough energy to break all of the principle bonds in an organic molecule. The difference spectrum between treated to untreated samples appears to be fitted well using specific component spectra from these groups of compounds. Increases in NMR peak amplitudes are observed and appear to be correlated with the spectral locations of several amino acids, membrane components and several sugars/saccharides. Increases in peak intensities of 4-8% were observed in the 0.8-1.1 ppm chemical shift region, characteristic of lipid and amino acid groups. A 3.5-4% increase was observed in the 2 ppm and 3.4-4 ppm region characteristic of

  12. Thermochemistry of Proton-Coupled Electron Transfer Reagents and its Implications

    SciTech Connect

    Warren, Jeffrey J.; Tronic, Tristan A.; Mayer, James M.

    2010-12-08

    Many, if not most, redox reactions are coupled to proton transfers. This includes most common sources of chemical potential energy, from the bioenergetic processes that power cells to the fossil fuel combustion that powers cars. These proton-coupled electron transfer or PCET processes may involve multiple electrons and multiple protons, as in the 4 e–, 4 H+ reduction of dioxygen (O2) to water (eq 1), or can involve one electron and one proton such as the formation of tyrosyl radicals from tyrosine residues (TyrOH) in enzymatic catalytic cycles (eq 2). In addition, many multi-electron, multi-proton processes proceed in one-electron and one-proton steps. Organic reactions that proceed in one-electron steps involve radical intermediates, which play critical roles in a wide range of chemical, biological, and industrial processes. This broad and diverse class of PCET reactions are central to a great many chemical and biochemical processes, from biological catalysis and energy transduction, to bulk industrial chemical processes, to new approaches to solar energy conversion. PCET is therefore of broad and increasing interest, as illustrated by this issue and a number of other recent reviews.

  13. Nickel phlorin intermediate formed by proton-coupled electron transfer in hydrogen evolution mechanism

    PubMed Central

    Solis, Brian H.; Maher, Andrew G.; Dogutan, Dilek K.; Nocera, Daniel G.; Hammes-Schiffer, Sharon

    2016-01-01

    The development of more effective energy conversion processes is critical for global energy sustainability. The design of molecular electrocatalysts for the hydrogen evolution reaction is an important component of these efforts. Proton-coupled electron transfer (PCET) reactions, in which electron transfer is coupled to proton transfer, play an important role in these processes and can be enhanced by incorporating proton relays into the molecular electrocatalysts. Herein nickel porphyrin electrocatalysts with and without an internal proton relay are investigated to elucidate the hydrogen evolution mechanisms and thereby enable the design of more effective catalysts. Density functional theory calculations indicate that electrochemical reduction leads to dearomatization of the porphyrin conjugated system, thereby favoring protonation at the meso carbon of the porphyrin ring to produce a phlorin intermediate. A key step in the proposed mechanisms is a thermodynamically favorable PCET reaction composed of intramolecular electron transfer from the nickel to the porphyrin and proton transfer from a carboxylic acid hanging group or an external acid to the meso carbon of the porphyrin. The C–H bond of the active phlorin acts similarly to the more traditional metal-hydride by reacting with acid to produce H2. Support for the theoretically predicted mechanism is provided by the agreement between simulated and experimental cyclic voltammograms in weak and strong acid and by the detection of a phlorin intermediate through spectroelectrochemical measurements. These results suggest that phlorin species have the potential to perform unique chemistry that could prove useful in designing more effective electrocatalysts. PMID:26655344

  14. Probing Nonadiabaticity in the Proton-Coupled Electron Transfer Reaction Catalyzed by Soybean Lipoxygenase

    PubMed Central

    2014-01-01

    Proton-coupled electron transfer (PCET) plays a vital role in many biological and chemical processes. PCET rate constant expressions are available for various well-defined regimes, and determining which expression is appropriate for a given system is essential for reliable modeling. Quantitative diagnostics have been devised to characterize the vibronic nonadiabaticity between the electron–proton quantum subsystem and the classical nuclei, as well as the electron–proton nonadiabaticity between the electrons and proton(s) within the quantum subsystem. Herein these diagnostics are applied to a model of the active site of the enzyme soybean lipoxygenase, which catalyzes a PCET reaction that exhibits unusually high deuterium kinetic isotope effects at room temperature. Both semiclassical and electronic charge density diagnostics illustrate vibronic and electron–proton nonadiabaticity for this PCET reaction, supporting the use of the Golden rule nonadiabatic rate constant expression with a specific form of the vibronic coupling. This type of characterization will be useful for theoretical modeling of a broad range of PCET processes. PMID:25258676

  15. Transverse Mode-Coupling Instability in the CERN Super Proton Synchrotron

    NASA Astrophysics Data System (ADS)

    Métral, E.; Arduini, G.; Benedetto, E.; Burkhardt, H.; Shaposhnikova, E.; Rumolo, G.

    2005-06-01

    A vertical single-bunch instability has been observed in 2003 right after injection at 26 GeV/c in the CERN Super Proton Synchrotron (SPS). High-intensity proton bunches (˜1.2 1011 p/b) with low longitudinal emittance (˜0.2 eVs) are affected by heavy losses after less than one synchrotron period. Such phenomenon has already been observed with leptons in many machines, e.g. in the SPS, or with protons at transition, e.g. in the CERN Proton Synchrotron (PS). However, to the authors' knowledge, it is the first time with protons far from transition. The absence of transverse mode-coupling instability in hadron machines is generally explained by three mechanisms: (i) the intensity threshold for the longitudinal microwave instability is generally lower than for the transverse mode-coupling instability, (ii) the intensity threshold due to mode-coupling between the two lowest azimuthal modes increases with space charge, and (iii) the intensity threshold increases with bunch length (in the long-bunch regime). In this talk measurements performed in the SPS are compared to analytical and simulation predictions.

  16. Modulation of Proton-Coupled Electron Transfer through Molybdenum-Quinonoid Interactions.

    PubMed

    Henthorn, Justin T; Agapie, Theodor

    2016-06-01

    An expanded series of π-bound molybdenum-quinonoid complexes supported by pendant phosphines has been synthesized. These compounds formally span three protonation-oxidation states of the quinonoid fragment (catechol, semiquinone, quinone) and two different oxidation states of the metal (Mo(0), Mo(II)), notably demonstrating a total of two protons and four electrons accessible in the system. Previously, the reduced Mo(0)-catechol complex 1 and its reaction with dioxygen to yield the two-proton/two-electron oxidized Mo(0)-quinone compound 4 was explored, while, herein, the expansion of the series to include the two-electron oxidized Mo(II)-catechol complex 2, the one-proton/two-electron oxidized Mo-semiquinone complex 3, and the two-proton/four-electron oxidized Mo(II)-quinone complexes 5 and 6 is reported. Transfer of multiple equivalents of protons and electrons from the Mo(0) and Mo(II) catechol complexes, 1 and 2, to H atom acceptor TEMPO suggests the presence of weak O-H bonds. Although thermochemical analyses are hindered by the irreversibility of the electrochemistry of the present compounds, the reactivity observed suggests weaker O-H bonds compared to the free catechol, indicating that proton-coupled electron transfer can be facilitated significantly by the π-bound metal center. PMID:27227812

  17. Thermochemistry of Proton-Coupled Electron Transfer Reagents and its Implications

    SciTech Connect

    Warren, Jeffrey J; Tronic, Tristan A; Mayer, James M

    2010-01-01

    The primary goals of this review are (1) to assemble thermochemical data—reduction potentials, pK{sub a} values, and bond dissociation free energies and enthalpies—from disparate sources and (2) to illustrate the utility of these data in understanding proton-coupled redox chemistry. We hope to have illustrated the value and power of thermochemical cycles (“square schemes”).

  18. The HP-1 maquette: From an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange

    PubMed Central

    Huang, Steve S.; Koder, Ronald L.; Lewis, Mitchell; Wand, A. Joshua; Dutton, P. Leslie

    2004-01-01

    Synthetic heme-binding four-α-helix bundles show promise as working model systems, maquettes, for understanding heme cofactor–protein assembly and function in oxidoreductases. Despite successful inclusion of several key functional elements of natural proteins into a family of heme protein maquettes, the lack of 3D structures, due principally to conformational heterogeneity, has prevented them from achieving their full potential. We report here the design and synthesis of HP-1, a disulfide-bridged two-α-helix peptide that self-assembles to form an antiparallel twofold symmetric diheme four-α-helix bundle protein with a stable conformation on the NMR time-scale. The HP-1 design strategy began with the x-ray crystal structure of the apomaquette L31M, an apomaquette derived from the structurally heterogeneous tetraheme-binding H10H24 prototype. L31M was functionally redesigned to accommodate two hemes ligated to histidines and to retain the strong coupling of heme oxidation-reduction to glutamate acid–base transitions and proton exchange that was characterized in molten globule predecessors. Heme insertion was modeled with angular constraints statistically derived from natural proteins, and the pattern of hydrophobic and hydrophilic residues on each helix was then altered to account for this large structural reorganization. The transition to structured holomaquette involved the alteration of 6 of 31 residues in each of the four identical helices and, unlike our earlier efforts, required no design intermediates. Oxidation-reduction of both hemes displays an unusually low midpoint potential (–248 mV vs. normal hydrogen electrode at pH 9.0), which is strongly coupled to proton binding, as designed. PMID:15056758

  19. Proton NMR studies of the electronic structure of ZrH/sub x/

    NASA Technical Reports Server (NTRS)

    Attalla, A.; Bowman, R. C., Jr.; Craft, B. D.; Venturini, E. L.; Rhim, W. K.

    1982-01-01

    The proton spin lattice relaxation times and Knight shifts were measured in f.c.c. (delta-phase) and f.c.t. (epsilon-phase) ZrH/sub x/ for 1.5 or = to x or = to 2.0. Both parameters indicate that N(E/sub F/) is very dependent upon hydrogen content with a maximum occurring at ZrH1 83. This behavior is ascribed to modifications in N(E/sub F/) through a fcc/fct distortion in ZrH/sub x/ associated with a Jahn-Teller effect.

  20. Isotope-edited proton NMR study on the structure of a pepsin/inhibitor complex

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Erickson, J.W.; Abad-Zapatero, C.

    1988-11-01

    A general approach is illustrated for providing detailed structural information on large enzyme/inhibitor complexes using NMR spectroscopy. The method involves the use of isotopically labeled ligands to simplify two-dimensional NOE spectra of large molecular complexes by isotope-editing techniques. With this approach, the backbone and side-chain conformations (at the P/sub 2/ and P/sub 3/ sites) of a tightly bound inhibitor of porcine pepsin have bene determined. In addition, structural information on the active site of pepsin has been obtained. Due to the sequence homology between porcine pepsin and human renin, this structural information may prove useful for modeling renin/inhibitor complexes with the ultimate goal of designing more effective renin inhibitors. Moreover, this general approach can be applied to study other biological systems of interest such as other enzyme/inhibitor complexes, ligands bound to soluble receptors, and enzyme/substrate interactions.

  1. Proton decoupling and recoupling under double-nutation irradiation in solid-state NMR

    SciTech Connect

    Takeda, Kazuyuki Wakisaka, Asato; Takegoshi, K.

    2014-12-14

    The effect of {sup 1}H decoupling in magic-angle spinning solid-state NMR is studied under radiofrequency irradiation causing simultaneous nutations around a pair of orthogonal axes. Double-nutation with an arbitrary pair of nutation frequencies is implemented through modulation of the amplitude, phase, and frequency of the transmitting pulses. Similarity and difference of double-nutation decoupling and two-pulse phase-modulation decoupling schemes [A. E. Bennett, C. M. Rienstra, M. Auger, K. V. Lakshmi, and R. G. Griffin, J. Chem. Phys. 103, 6951–6958 (1995) and I. Scholz, P. Hodgkinson, B. H. Meier, and M. Ernst, J. Chem. Phys. 130, 114510 (2009)] are discussed. The structure of recoupling bands caused by interference of the {sup 1}H spin nutation with sample spinning is studied by both experiments and numerical simulations.

  2. Proton decoupling and recoupling under double-nutation irradiation in solid-state NMR

    NASA Astrophysics Data System (ADS)

    Takeda, Kazuyuki; Wakisaka, Asato; Takegoshi, K.

    2014-12-01

    The effect of 1H decoupling in magic-angle spinning solid-state NMR is studied under radiofrequency irradiation causing simultaneous nutations around a pair of orthogonal axes. Double-nutation with an arbitrary pair of nutation frequencies is implemented through modulation of the amplitude, phase, and frequency of the transmitting pulses. Similarity and difference of double-nutation decoupling and two-pulse phase-modulation decoupling schemes [A. E. Bennett, C. M. Rienstra, M. Auger, K. V. Lakshmi, and R. G. Griffin, J. Chem. Phys. 103, 6951-6958 (1995) and I. Scholz, P. Hodgkinson, B. H. Meier, and M. Ernst, J. Chem. Phys. 130, 114510 (2009)] are discussed. The structure of recoupling bands caused by interference of the 1H spin nutation with sample spinning is studied by both experiments and numerical simulations.

  3. Sensitivity enhancement of remotely coupled NMR detectors using wirelessly powered parametric amplification.

    PubMed

    Qian, Chunqi; Murphy-Boesch, Joseph; Dodd, Stephen; Koretsky, Alan

    2012-09-01

    A completely wireless detection coil with an integrated parametric amplifier has been constructed to provide local amplification and transmission of MR signals. The sample coil is one element of a parametric amplifier using a zero-bias diode that mixes the weak MR signal with a strong pump signal that is obtained from an inductively coupled external loop. The NMR sample coil develops current gain via reduction in the effective coil resistance. Higher gain can be obtained by adjusting the level of the pumping power closer to the oscillation threshold, but the gain is ultimately constrained by the bandwidth requirement of MRI experiments. A feasibility study here shows that on a NaCl/D(2) O phantom, (23) Na signals with 20 dB of gain can be readily obtained with a concomitant bandwidth of 144 kHz. This gain is high enough that the integrated coil with parametric amplifier, which is coupled inductively to external loops, can provide sensitivity approaching that of direct wire connection. PMID:22246567

  4. Sensitivity Enhancement of Remotely Coupled NMR Detectors using Wirelessly Powered Parametric Amplification

    PubMed Central

    Qian, Chunqi; Murphy-Boesch, Joseph; Dodd, Stephen; Koretsky, Alan

    2011-01-01

    A completely wireless detection coil with an integrated parametric amplifier has been constructed to provide local amplification and transmission of MR signals. The sample coil is one element of a parametric amplifier using a zero-bias diode that mixes the weak MR signal with a strong pump signal that is obtained from an inductively coupled external loop. The NMR sample coil develops current gain via reduction in the effective coil resistance. Higher gain can be obtained by adjusting the level of the pumping power closer to the oscillation threshold, but the gain is ultimately constrained by the bandwidth requirement of MRI experiments. A feasibility study here shows that on a NaCl/D2O phantom, 23Na signals with 20 dB of gain can be readily obtained with a concomitant bandwidth of 144 kHz. This gain is high enough that the integrated coil with parametric amplifier, which is coupled inductively to external loops, can provide sensitivity approaching that of direct wire connection. PMID:22246567

  5. The stereospecific assignment of H5' and H5' in RNA using the sign of two-bond carbon-proton scalar couplings

    SciTech Connect

    Hines, J.V.; Varani, G.; Landry, S.M.; Tinoco, I. Jr. )

    1993-11-17

    Stereospecific assignment of H5' and H5' protons in the NMR spectra of nucleic acids provides significant improvement in the use of NOE distance and torsion angle constraints for structure determination. With stereospecific assignments, the torsion angles [beta] (P5'-O5'-C5'-C4') and [gamma] (O5'-C5'-C4'-C3') can be determined on the basis of [sup 1]H-[sup 1]H and [sup 31]P-[sup 1]H couplings. In addition, stereospecific assignment allows use of NOE distance constraints for H5' and H5'. We report a novel, independent method for the stereospecific assignment of the H5' (pro-S) and H5' (pro-R) protons which is based only on the sign of the carbon-proton two-bond scalar couplings and will not be greatly limited by line width. The sign of [sup 2]J[sub CH] can also be used to determine torsion angle [gamma] and the sugar conformation. Determination of the sign of the two-bond carbon-proton couplings provides a useful new method for the structure determination of RNA molecules. The ribose sugar conformation and torsion angle [gamma] (O5'-C5'-C4'-C3') can be specified. Furthermore, H5' and H5' protons can be stereospecifically assigned, allowing their use in NOE distance constraints and in determining [beta] (P5'-O5'-C5'-C4'). The correlation we have reported between the sign of [sup 2]J[sub CH] and RNA structure will be particularly useful in the study of large RNAs and RNA-protein complexes. 21 refs., 1 fig., 1 tab.

  6. The differences in the T2 relaxation rates of the protons in the partially-deuteriated and fully protonated sugar residues in a large oligo-DNA ('NMR-window') gives complementary structural information.

    PubMed Central

    Agback, P; Maltseva, T V; Yamakage, S I; Nilson, F P; Földesi, A; Chattopadhyaya, J

    1994-01-01

    Selective incorporation of the stereospecifically deuteriated sugar moieties (> 97 atom % 2H enhancements at H2', H2'', H3' and H5'/5'' sites, approximately 85 atom % 2H enhancement at H4' and approximately 20 atom % 2H enhancement at H1') in DNA and RNA by the 'NMR-window' approach has been shown to solve the problem of the resonance overlap [refs. 1, 2 & 3]. Such specific deuterium labelling gives much improved resolution and sensitivity of the residual sugar proton (i.e. H1' or H4') vicinal to the deuteriated centers (ref. 3). The T2 relaxation time of the residual protons also increases considerably in the partially-deuteriated (shown by underline) sugar residues in dinucleotides [d(CpG), d(GpC), d(ApT), d(TpA)], trinucleotide r(A2'p5'A2'p5'A) and 20-mer DNA duplex 5'd(C1G2C3-G4C5G6C7G8A9A10T11T12C13G14C15G16C17G18C19G20)(2) 3'. The protons with shorter T2 can be filtered away using a number of different NMR experiments such as ROESY, MINSY or HAL. The NOE intensity of the cross-peaks in these experiments includes only straight pathway from H1' to aromatic proton (i-i and i-i + 1) without any spin-diffusion. The volumes of these NOE cross-peaks could be measured with high accuracy as their intensity is 3 to 4 times larger than the corresponding peaks in the fully protonated residues in the normal NOESY spectra. The structural informations thus obtainable from the residual protons in the partially-deuteriated part of the duplex and the fully protonated part in the 'NMR window' can indeed complement each other. PMID:8190632

  7. Proton NMR investigation of the heme active site structure of an engineered cytochrome c peroxidase that mimics manganese peroxidase.

    PubMed

    Wang, X; Lu, Y

    1999-07-13

    The heme active site structure of an engineered cytochrome c peroxidase [MnCcP; see Yeung, B. K., et al. (1997) Chem. Biol. 4, 215-221] that closely mimics manganese peroxidase (MnP) has been characterized by both one- and two-dimensional NMR spectroscopy. All hyperfine-shifted resonances from the heme pocket as well as resonances from catalytically relevant amino acid residues in the congested diamagnetic envelope have been assigned. From the NMR spectral assignment and the line broadening pattern of specific protons in NOESY spectra of MnCcP, the location of the engineered Mn(II) center is firmly identified. Furthermore, we found that the creation of the Mn(II)-binding site in CcP resulted in no detectable structural changes on the distal heme pocket of the protein. However, notable structural changes are observed at the proximal side of the heme cavity. Both CepsilonH shift of the proximal histidine and (15)N shift of the bound C(15)N(-) suggest a weaker heme Fe(III)-N(His) bond in MnCcP compared to WtCcP. Our results indicate that the engineered Mn(II)-binding site in CcP resulted in not only a similar Mn(II)-binding affinity and improved MnP activity, but also weakened the Fe(III)-N(His) bond strength of the template protein CcP so that its bond strength is similar to that of the target protein MnP. The results presented here help elucidate the impact of designing a metal-binding site on both the local and global structure of the enzyme, and provide a structural basis for engineering the next generation of MnCcP that mimics MnP more closely. PMID:10413489

  8. HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.

    PubMed

    Cornilescu, Gabriel; Bahrami, Arash; Tonelli, Marco; Markley, John L; Eghbalnia, Hamid R

    2007-08-01

    We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic

  9. Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

    DOE PAGESBeta

    Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John -Paul; Schrader, Tobias E.; Ostermann, Andreas; Kovalevsky, Andrey Y.; McKenna, Robert; Fisher, Suzanne Zoe

    2015-05-05

    Proton transfer is a fundamental mechanism at the core of many enzyme-catalyzed reactions. It is also exquisitely sensitive to a number of factors, including pH, electrostatics, proper active-site geometry, and chemistry. Carbonic anhydrase has evolved a fast and efficient way to conduct protons through a combination of hydrophilic amino acid side chains that coordinate a highly ordered H-bonded water network. This study uses a powerful approach, combining NMR solution studies with neutron protein crystallography, to determine the effect of pH and divalent cations on key residues involved in proton transfer in human carbonic anhydrase. Lastly, the results have broad implicationsmore » for our understanding of proton transfer and how subtle changes in ionization and H-bonding interactions can modulate enzyme catalysis.« less

  10. Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

    SciTech Connect

    Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John -Paul; Schrader, Tobias E.; Ostermann, Andreas; Kovalevsky, Andrey Y.; McKenna, Robert; Fisher, Suzanne Zoe

    2015-05-05

    Proton transfer is a fundamental mechanism at the core of many enzyme-catalyzed reactions. It is also exquisitely sensitive to a number of factors, including pH, electrostatics, proper active-site geometry, and chemistry. Carbonic anhydrase has evolved a fast and efficient way to conduct protons through a combination of hydrophilic amino acid side chains that coordinate a highly ordered H-bonded water network. This study uses a powerful approach, combining NMR solution studies with neutron protein crystallography, to determine the effect of pH and divalent cations on key residues involved in proton transfer in human carbonic anhydrase. Lastly, the results have broad implications for our understanding of proton transfer and how subtle changes in ionization and H-bonding interactions can modulate enzyme catalysis.

  11. United Atom Rotational Coupling in Proton + Helium Collision

    NASA Astrophysics Data System (ADS)

    Wang, Chiiling

    United-atom 2p(sigma)-2p(pi) rotational coupling in asymmetric collisions is influenced by an avoided crossing between the 2p(sigma) and 2s(sigma) orbitals. This influence is studied using the HeH('+) system as a prototype. In (SIGMA)(,2)-(SIGMA)(,3)-(pi)(,1) three-state calculations, the time-dependent Schrodinger equation is solved numerically. Substantial population of the 2s(sigma) state is found, which disagrees with the estimates based on the Landau-Zener model. The (SIGMA)(,3) level is populated directly by transitions near the avoided crossing at b = 0.4 au and indirectly by (SIGMA)(,2)-(pi)(,1)-(SIGMA)(,3) rotational coupling for b > 0.4 au. The ratios of P(,(SIGMA)(,3))(b)/ P(,(SIGMA)(,3))(b) + P(,(pi)(,1))(b) are calculated and compared with Dr. R. Hippler's experimental data. A six-state calculation, in the basis of (SIGMA)(,1), (SIGMA)(,2), (SIGMA)(,3), (SIGMA)(,4), (pi)(,1) and (pi)(,2) molecular states, is also made. Cross sections and alignment and orientation parameters have been computed from the transition amplitudes for various energies.

  12. H1 NMR study of proton dynamics in Cs5H3(SO4)4•xH2O

    NASA Astrophysics Data System (ADS)

    Suzuki, Koh-Ichi; Hayashi, Shigenobu

    2006-10-01

    Complicated phase relations in Cs5H3(SO4)4•xH2O are revealed by thermal analyses. A superprotonic phase transition takes place at 420K for both the hydrated and the anhydrous forms. The H1 magic-angle-spinning (MAS) NMR spectra were traced at room temperature and at Larmor frequency of 400.13MHz . The H1 chemical shifts of the acidic protons are 10.9 and 11.2ppm for the hydrated and the anhydrous forms, respectively. The hydrated sample shows a signal at 9.7ppm additionally, which is ascribed to H3O+ . Proton dynamics has been studied by H1 static NMR spectra and spin-lattice relaxation times, T1 . In both a room-temperature phase (phase RT) and a high-temperature phase (phase HT), translational diffusion of protons takes place. The H1 mean residence times in phase RT are obtained from the second moment analysis; Ea=49kJmol-1 and τ0=1.8×10-11s for the anhydrous form and Ea=31kJmol-1 and τ0=2.2×10-9s for the hydrated form. From the analysis of H1 T1 results we have obtained parameters of proton diffusion for phase HT; Ea=34kJmol-1 and τ0=3×10-13s for the anhydrous form and Ea=36kJmol-1 and τ0=3×10-14s for the hydrated form. In both phases, protons diffuse faster in the hydrated form than in the anhydrous form. The proton conductivities estimated from the NMR results for the anhydrous form agree with the macroscopic values in literature.

  13. Proton NMR study of molecular dynamics in ammonium tribromo stannate (NH 4SnBr 3)

    NASA Astrophysics Data System (ADS)

    Ramesh, K. P.; Devaraj, N.; Ramakrishna, J.; Venu, K.; Sastry, V. S. S.

    1993-11-01

    The proton second moment M2 and spin-lattice relaxation time T1 have been measured in ammonium tribromo stannate (NH 4SnBr 3) in the temperature range 77-300 K, to determine the ammonium dynamics. The continuous wave signal is strong and narrow at 77 and 300 K but has revealed an interesting intensity anomaly between 210 and 125 K. T1 shows a maximum (13 s) around 220 K. No minimum in the T1 vs 1000/ T plot was observed down to 77 K. M2 and T1 results are interpreted in terms of NH +4 ion dynamics. The activation energy Ea for NH +4 ion reorientation is estimated to be 1.4 kcal mol -1.

  14. Proton NMR analysis of octane number for motor gasoline: Part V

    SciTech Connect

    Ichikawa, M.; Nonaka, N.; Amano, H.; Takada, I.; Ishimori, S.; Andoh, H.; Kumamoto, K.

    1992-10-01

    A method to predict the octane number of automobile gasoline containing methyl tert-butyl ether (MTBE) by proton magnetic resonance (PMR) spectrometry was studied. Samples of gasoline whose octane numbers had been identified according to the ASTM standards (commercially available premium gasoline to which MTBE was added at rates of 7 vol % and 14 vol %) were used in this investigation of the effect of MTBE on the octane number. The findings were utilized to introduce a term regarding MTBE into the previously reported linear regression equation for estimating the octane number from the PMR spectrum, and the appropriateness of the linear regression equation was assessed. As a result the MTBE contents in the sample were determined with satisfactory accuracy by using a standard addition method, and a linear regression equation reflecting the effect of MTBE was obtained. These achievements are reported. 11 refs., 3 figs., 5 tabs.

  15. The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase.

    PubMed Central

    Kannt, A; Lancaster, C R; Michel, H

    1998-01-01

    We have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in Paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. Subsequent Monte Carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. Inclusion of a model membrane allowed us to restrict the calculations to the functionally essential subunits I and II. Some residues were calculated to have complex titration curves, as a result of strong electrostatic coupling, desolvation, and dipolar interactions. Around the heme a3-CuB binuclear center, we have identified a cluster of 18 strongly interacting residues that account for most of the proton uptake linked to electron transfer. This was calculated to be between 0.7 and 1.1 H+ per electron, depending on the redox transition considered. A hydroxide ion bound to CuB was determined to become protonated to form water upon transfer of the first electron to the binuclear site. The bulk of the protonation changes linked to further reduction of the heme a3-CuB center was calculated to be due to proton uptake by the interacting cluster and Glu(II-78). Upon formation of the three-electron reduced state (P1), His325, modeled in an alternative orientation away from CuB, was determined to become protonated. The agreement of these results with experiment and their relevance in the light of possible mechanisms of redox-coupled proton transfer are discussed. PMID:9533684

  16. The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase.

    PubMed

    Kannt, A; Lancaster, C R; Michel, H

    1998-02-01

    We have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in Paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. Subsequent Monte Carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. Inclusion of a model membrane allowed us to restrict the calculations to the functionally essential subunits I and II. Some residues were calculated to have complex titration curves, as a result of strong electrostatic coupling, desolvation, and dipolar interactions. Around the heme a3-CuB binuclear center, we have identified a cluster of 18 strongly interacting residues that account for most of the proton uptake linked to electron transfer. This was calculated to be between 0.7 and 1.1 H+ per electron, depending on the redox transition considered. A hydroxide ion bound to CuB was determined to become protonated to form water upon transfer of the first electron to the binuclear site. The bulk of the protonation changes linked to further reduction of the heme a3-CuB center was calculated to be due to proton uptake by the interacting cluster and Glu(II-78). Upon formation of the three-electron reduced state (P1), His325, modeled in an alternative orientation away from CuB, was determined to become protonated. The agreement of these results with experiment and their relevance in the light of possible mechanisms of redox-coupled proton transfer are discussed. PMID:9533684

  17. Insights into proton-coupled electron transfer mechanisms of electrocatalytic H2 oxidation and production

    PubMed Central

    Horvath, Samantha; Fernandez, Laura E.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2012-01-01

    The design of molecular electrocatalysts for H2 oxidation and production is important for the development of alternative renewable energy sources that are abundant, inexpensive, and environmentally benign. Recently, nickel-based molecular electrocatalysts with pendant amines that act as proton relays for the nickel center were shown to effectively catalyze H2 oxidation and production. We developed a quantum mechanical approach for studying proton-coupled electron transfer processes in these types of molecular electrocatalysts. This theoretical approach is applied to a nickel-based catalyst in which phosphorous atoms are directly bonded to the nickel center, and nitrogen atoms of the ligand rings act as proton relays. The catalytic step of interest involves electron transfer between the nickel complex and the electrode as well as intramolecular proton transfer between the nickel and nitrogen atoms. This process can occur sequentially, with either the electron or proton transferring first, or concertedly, with the electron and proton transferring simultaneously without a stable intermediate. The electrochemical rate constants are calculated as functions of overpotential for the concerted electron-proton transfer reaction and the two electron transfer reactions in the sequential mechanisms. Our calculations illustrate that the concerted electron-proton transfer standard rate constant will increase as the equilibrium distance between the nickel and nitrogen atoms decreases and as the pendant amines become more flexible to facilitate the contraction of this distance with a lower energy penalty. This approach identifies the favored mechanisms under various experimental conditions and provides insight into the impact of substituents on the nitrogen and phosphorous atoms. PMID:22529352

  18. Using Pseudocontact Shifts and Residual Dipolar Couplings as Exact NMR Restraints for the Determination of Protein Structural Ensembles.

    PubMed

    Camilloni, Carlo; Vendruscolo, Michele

    2015-12-29

    Nuclear magnetic resonance (NMR) spectroscopy provides detailed information about the structure and dynamics of proteins by exploiting the conformational dependence of the magnetic properties of certain atomic nuclei. The mapping between NMR measurements and molecular structures, however, often requires approximated descriptions based on the fitting of a number of parameters, thus reducing the quality of the information available from the experiments. To improve on this limitation, we show here that it is possible to use pseudocontact shifts and residual dipolar couplings as "exact" NMR restraints. We implement this strategy by using a replica-averaging method and illustrate its application by calculating an ensemble of structures representing the dynamics of the two-domain protein calmodulin. PMID:26624789

  19. High-Speed Magic-Angle Spinning 13C MAS NMR Spectra of Adamantane: Self-Decoupling of the Heteronuclear Scalar Interaction and Proton Spin Diffusion

    NASA Astrophysics Data System (ADS)

    Ernst, Matthias; Verhoeven, Aswin; Meier, Beat H.

    1998-02-01

    We have investigated the carbon line shape of solid adamantane under high-speed magic-angle sample spinning (MAS) acquired without proton decoupling. The CH-group shows a spinning-speed-dependent line broadening while the CH2-group consists of a spinning-speed-independent sharp component and a spinning-speed-dependent broader part. These phenomena can be explained by self-decoupling of theJ-interaction due to proton spin diffusion. Such a self-decoupling process can be described by a magnetization exchange process between the multiplet lines. Changing the spin-diffusion rate constant by off-resonance irradiation of the protons allows us to observe the full range from slow exchange to coalescence to fast exchange of the carbon spectra. One of the multiplet components in the CH2-group corresponds to a group spin of the protons of zero and therefore does not couple to the other protons. This gives rise to the sharp central line. The magnetization exchange rate constant between the different multiplet lines can be determined from the spectra and is a measure for the spinning-speed-dependent proton spin-diffusion rate constant. Even at an MAS speed of 30 kHz, proton spin diffusion is still observable despite the relatively weak intermolecular proton dipolar-coupling network in adamantane which results in a static proton line width of only 14 kHz (full width at half height).

  20. The effects of bone on proton NMR relaxation times of surrounding liquids

    NASA Technical Reports Server (NTRS)

    Davis, C. A.; Genant, H. K.; Dunham, J. S.

    1986-01-01

    Preliminary attempts by our group at UCSF to assess fat content of vertebral marrow in the lumbar spine using relaxation time information demonstrated that the presence of trabecular bone affects relaxation times. The objective of this work was a thorough study of the effects of bone on NMR relaxation characteristics of surrounding liquids. Trabecular bone from autopsy specimens was ground up and sifted into a series of powders with graded densities ranging from 0.3 gm/cc to 0.8 gm/cc. Each powder was placed first in n-saline and then in cottonseed oil. With spectroscopy, spin-lattice relaxation times (T1) and effective spin-spin relaxation times (T2*) were measured for each liquid in each bone powder. As bone density and surface to volume ratio increased, T1 decreased faster for saline than for oil. T2* decreased significantly for both water and oil as the surface to volume ratio increased. It was concluded that effects of water on T1 could be explained by a surface interaction at the bone/liquid interface, which restricted rotational and translational motion of nearby molecules. The T1s of oil were not affected since oil molecules are nonpolar, do not participate in significant intermolecular hydrogen bonding, and therefore would not be expected to interact strongly with the bone surface. Effects on T2* could be explained by local magnetic field inhomogeneities created by discontinuous magnetic susceptibility near the bone surface. These preliminary results suggest that water in contact with trabecular bone in vivo will exhibit shortened relaxation times.

  1. Characterization of pH titration shifts for all the nonlabile proton resonances in a protein by two-dimensional NMR: The case of mouse epidermal growth factor

    SciTech Connect

    Kohda, Daisuke; Sawada, Toshie; Inagaki, Fuyuhiko )

    1991-05-21

    The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p{sup 2}H range 1.5-9 with two-dimensional (2D) {sup 1}H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable group which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups ({alpha}-amino group, four Asp, two Glu, one His, and {alpha}-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal {alpha}-amino group induced a widespread conformational change over the {beta}-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. The authors found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins.

  2. Characterization of pH titration shifts for all the nonlabile proton resonances a protein by two-dimensional NMR: the case of mouse epidermal growth factor.

    PubMed

    Kohda, D; Sawada, T; Inagaki, F

    1991-05-21

    The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p2H range 1.5-9 with two-dimensional (2D) 1H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable groups which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups (alpha-amino group, four Asp, two Glu, one His, and alpha-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal alpha-amino group induced a widespread conformational change over the beta-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. We found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins. PMID:2036358

  3. The Peculiarities of the NMR Spin-Lattice Relaxation in Proton Exchanged LINBO_{3}

    NASA Astrophysics Data System (ADS)

    Vertegel, Igor; Chesnokov, Eugeny; Ovcharenko, Alexander; Vertegel, Ivan

    2013-06-01

    The temperature dependence of the spin-lattice relaxation time T_{1} of Li^{7} nuclei in the temperature range (170-430 K) was investigated in LiNbO_{3} polycrystalline samples: the clean and annealed ones in a hydrogen environment at temperature around 1000° C. The anomaly in the temperature dependence of T_{1} was found in range 300-340 K for both pure and annealed crystals. The reduction of the time T_{1} in the annealed lithium niobate crystal is caused by the creation of point defects (F^{+} or F-centers), with the dominant F-centers contribution. An increase in the activation energy in the annealed crystal can be explained by the following. It is known for the pure lithium niobate that an oscillation of lithium occurs in a symmetrical potential consisting of three wells. Formation of the oxygen vacancies in the annealed crystals is accompanied with extrinsic protons occupation of the vacancies. It leads to the symmetry violation and causes an i ncrease of the activation barrier.

  4. Proton NMR analysis of octane number for motor gasoline: Part IV

    SciTech Connect

    Ichikawa, M.; Nonaka, N.; Amano, H.; Takada, I.; Ishimori, S.; Andoh, H.; Kumamoto, K.

    1992-08-01

    Software for predicting the octane number of motor gasoline by proton magnetic resonance (PMR) spectrometry has been formulated. At the same time, a method has been studied to predict the composition of gasoline (in terms of the contents of paraffin, olefin, and aromatic compounds). The formulated program was evaluated by using it to predict the octane numbers of 31 samples of marketed summer gasoline (including 16 regular and 15 premium products), whose octane numbers and compositions were identified according to the ASTM standards. Also, the relationship between the PMR spectrum and gasoline composition was subjected to linear regression analysis by using the 31 samples whose octane numbers were calculated, and the appropriateness of the resultant regression equations was assessed. This report concerns the results of the study in which the octane numbers of the 31 samples were satisfactorily predicted by the formulated program and useful linear regression equation were obtained for the prediction of the composition of gasoline. 9 refs., 9 figs., 3 tabs.

  5. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I.

    PubMed

    Sazanov, Leonid A

    2014-08-01

    NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved "core" subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine. PMID:24943718

  6. Surface Proton Hopping and Coupling Pathway of Water Oxidation on Cobalt Oxide Catalyst

    NASA Astrophysics Data System (ADS)

    Pham, Hieu; Cheng, Mu-Jeng; Frei, Heinz; Wang, Lin-Wang

    We propose an oxidation pathway of water splitting on cobalt oxide surface with clear thermodynamic and kinetic details. The density-functional theory studies suggest that the coupled proton-electron transfer is not necessarily sequential and implicit in every elementary step of this mechanistic cycle. Instead, the initial O-O bond could be formed by the landing of water molecule on the surface oxos, which is then followed by the dispatch of protons through the hopping manner and subsequent release of di-oxygen. Our theoretical investigations of intermediates and transition states indicate that all chemical conversions in this pathway, including the proton transfers, are possible with low activation barriers, in addition to their favorable thermodynamics. Our hypothesis is supported by recent experimental observations of surface superoxide that is stabilized by hydrogen bonding to adjacent hydroxyl group, as an intermediate on fast-kinetics catalytic site.

  7. A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes

    NASA Astrophysics Data System (ADS)

    Velazquez Escobar, Francisco; Piwowarski, Patrick; Salewski, Johannes; Michael, Norbert; Fernandez Lopez, Maria; Rupp, Anna; Muhammad Qureshi, Bilal; Scheerer, Patrick; Bartl, Franz; Frankenberg-Dinkel, Nicole; Siebert, Friedrich; Andrea Mroginski, Maria; Hildebrandt, Peter

    2015-05-01

    Phytochromes are bimodal photoswitches composed of a photosensor and an output module. Photoactivation of the sensor is initiated by a double bond isomerization of the tetrapyrrole chromophore and eventually leads to protein conformational changes. Recently determined structural models of phytochromes identify differences between the inactive and the signalling state but do not reveal the mechanism of photosensor activation or deactivation. Here, we report a vibrational spectroscopic study on bathy phytochromes that demonstrates that the formation of the photoactivated state and thus (de)activation of the output module is based on proton translocations in the chromophore pocket coupling chromophore and protein structural changes. These proton transfer steps, involving the tetrapyrrole and a nearby histidine, also enable thermal back-isomerization of the chromophore via keto-enol tautomerization to afford the initial dark state. Thus, the same proton re-arrangements inducing the (de)activation of the output module simultaneously initiate the reversal of this process, corresponding to a negative feedback mechanism.

  8. Novel macrocyclic carriers for proton-coupled liquid membrane transport. Progress report, 1 December 1988--31 May 1991

    SciTech Connect

    Lamb, J.D.

    1991-06-10

    The objective of our research program is to elucidate the chemical principles which are responsible for the cation selectivity and permeability of liquid membranes containing macrocyclic carriers. Several new macrocyclic carriers were synthesized during the last three year period, including selenium-containing macrocycles, new crown-4 structures, and several new crown structures containing nitrogen based heterocycles as substituents in the principal macrocyclic ring. The cation binding properties of these macrocycles were investigated by potentiometric titration, calorimetric titration, solvent extraction, and NMR techniques. In addition, hydrophobic macrocycles were incorporated into dual hollow fiber membrane systems to investigate their membrane performance, especially in the proton-coupled transport mode. It was found that the dual hollow fiber system maintains the cation selectivity and permeability of supported liquid membranes, while enhancing membrane stability. The diffusion limited transport model was expanded to account for membrane solvent effects. Furthermore, Eu{sup 2+} transport was found to be similar to that of strontium and much higher than that of the lanthanides, in supported liquid membrane systems.

  9. Photochemical Tyrosine Oxidation with a Hydrogen-Bonded Proton Acceptor by Bidirectional Proton-Coupled Electron Transfer

    PubMed Central

    Pizano, Arturo A.; Yang, Jay L.

    2012-01-01

    Amino acid radical generation and transport are fundamentally important to numerous essential biological processes to which small molecule models lend valuable mechanistic insights. Pyridyl-amino acid-methyl esters are appended to a rhenium(I) tricarbonyl 1,10-phenanthroline core to yield rhenium–amino acid complexes with tyrosine ([Re]–Y–OH) and phenylalanine ([Re]–F). The emission from the [Re] center is more significantly quenched for [Re]–Y–OH upon addition of base. Time-resolved studies establish that excited-state quenching occurs by a combination of static and dynamic mechanisms. The degree of quenching depends on the strength of the base, consistent with a proton-coupled electron transfer (PCET) quenching mechanism. Comparative studies of [Re]–Y–OH and [Re]–F enable a detailed mechanistic analysis of a bidirectional PCET process. PMID:23495362

  10. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.

    PubMed

    Taraphder, Srabani; Maupin, C Mark; Swanson, Jessica M J; Voth, Gregory A

    2016-08-25

    The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II. PMID:27063577

  11. Molecular structure, tautomeric stability, protonation and deprotonation effects, vibrational, NMR and NBO analyses of 2,4-Dioxoimidazolidine-5-acetic acid (DOIAA) by quantum chemical calculations.

    PubMed

    Sridevi, C; Velraj, G

    2014-01-01

    This study represents the conformation, tautomeric stability, protonation and deprotonation effects, vibrational, electronic, NBO and NMR aspects of 2,4-Dioxoimidazolidine-5-acetic acid (DOIAA). Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. Tautomerism and the effect of solvent on the tautomeric equilibria in the gas phase and in different solvents were studied. The protonation and deprotonation effects on the reactivity and conformations of DOIAA were investigated. Electronic transitions were also studied and the most prominent transition corresponds to π→π*. Natural bond orbital (NBO) analysis was also carried out to find the intramolecular interactions and their stabilization energy. In DOIAA, the interaction between the lone pair donor orbital (n(LP1N5)) and the acceptor antibonding orbital π*(C6O7) reveals the strong stabilization energy of 224.9 kJ mol(-1). Molecular electrostatic potential (MEP) was calculated to predict the reactive sites of the title compound. The NMR results indicated that the observed chemical shifts for NH, COOH protons of DOIAA not only depend on the structure of the molecule being studied but also on the nature of the solvent, concentration of the sample and the presence of the other exchangeable protons. PMID:24291430

  12. Mixed Quantum-Classical Liouville Approach for Calculating Proton-Coupled Electron-Transfer Rate Constants.

    PubMed

    Shakib, Farnaz; Hanna, Gabriel

    2016-07-12

    In this work, we derive a general mixed quantum-classical formula for calculating thermal proton-coupled electron-transfer (PCET) rate constants, starting from the time integral of the quantum flux-flux correlation function. This formula allows for the direct simulation of PCET reaction dynamics via the mixed quantum-classical Liouville approach. Owing to the general nature of the derivation, this formula does not rely on any prior mechanistic assumptions and can be applied across a wide range of electronic and protonic coupling regimes. To test the validity of this formula, we applied it to a reduced model of a condensed-phase PCET reaction. Good agreement with the numerically exact rate constant is obtained, demonstrating the accuracy of our formalism. We believe that this approach constitutes a solid foundation for future investigations of the rates and mechanisms of a wide range of PCET reactions. PMID:27232936

  13. Composite-180° pulse-based symmetry sequences to recouple proton chemical shift anisotropy tensors under ultrafast MAS solid-state NMR spectroscopy.

    PubMed

    Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-01-01

    There is considerable interest in the measurement of proton ((1)H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong (1)H/(1)H dipolar interaction makes it difficult to determine small size (1)H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for (1)H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate γ-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple (1)H CSA in the indirect dimension of a 2D (1)H/(1)H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D (1)H/(1)H correlation spectrum without decoupling (1)H/(1)H dipolar couplings but by using ultrafast MAS rates up to 70 kHz. We successfully demonstrate that with a reasonable RF field requirement (<200 kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 270°0-90°180 composite-180° pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable (1)H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions. PMID:25497846

  14. Differentiation of enantiomers by 2D NMR spectroscopy at 1 T using residual dipolar couplings.

    PubMed

    Koos, Martin R M; Danieli, Ernesto; Casanova, Federico; Blümich, Bernhard; Luy, Burkhard

    2016-06-01

    Differentiating enantiomers using 2D bench-top NMR spectroscopy. Spectrometers working with permanent magnets at 1 T field strength allow the acquisition of 2D data sets. In conjunction with previously reported chiral alignment media, this setup allows the measurement of enantiomeric excess via residual dipolar couplings in stretched gelatine as a result of the reduced line width obtained by 2D J-resolved spectroscopy. PMID:25773020

  15. ATP-dependent substrate transport by the ABC transporter MsbA is proton-coupled.

    PubMed

    Singh, Himansha; Velamakanni, Saroj; Deery, Michael J; Howard, Julie; Wei, Shen L; van Veen, Hendrik W

    2016-01-01

    ATP-binding cassette transporters mediate the transbilayer movement of a vast number of substrates in or out of cells in organisms ranging from bacteria to humans. Current alternating access models for ABC exporters including the multidrug and Lipid A transporter MsbA from Escherichia coli suggest a role for nucleotide as the fundamental source of free energy. These models involve cycling between conformations with inward- and outward-facing substrate-binding sites in response to engagement and hydrolysis of ATP at the nucleotide-binding domains. Here we report that MsbA also utilizes another major energy currency in the cell by coupling substrate transport to a transmembrane electrochemical proton gradient. The dependence of ATP-dependent transport on proton coupling, and the stimulation of MsbA-ATPase by the chemical proton gradient highlight the functional integration of both forms of metabolic energy. These findings introduce ion coupling as a new parameter in the mechanism of this homodimeric ABC transporter. PMID:27499013

  16. ATP-dependent substrate transport by the ABC transporter MsbA is proton-coupled

    PubMed Central

    Singh, Himansha; Velamakanni, Saroj; Deery, Michael J.; Howard, Julie; Wei, Shen L.; van Veen, Hendrik W.

    2016-01-01

    ATP-binding cassette transporters mediate the transbilayer movement of a vast number of substrates in or out of cells in organisms ranging from bacteria to humans. Current alternating access models for ABC exporters including the multidrug and Lipid A transporter MsbA from Escherichia coli suggest a role for nucleotide as the fundamental source of free energy. These models involve cycling between conformations with inward- and outward-facing substrate-binding sites in response to engagement and hydrolysis of ATP at the nucleotide-binding domains. Here we report that MsbA also utilizes another major energy currency in the cell by coupling substrate transport to a transmembrane electrochemical proton gradient. The dependence of ATP-dependent transport on proton coupling, and the stimulation of MsbA-ATPase by the chemical proton gradient highlight the functional integration of both forms of metabolic energy. These findings introduce ion coupling as a new parameter in the mechanism of this homodimeric ABC transporter. PMID:27499013

  17. Analysis of kinetic isotope effects for proton-coupled electron transfer reactions.

    PubMed

    Edwards, Sarah J; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2009-03-12

    A series of rate constant expressions for nonadiabatic proton-coupled electron transfer (PCET) reactions are analyzed and compared. The approximations underlying each expression are enumerated, and the regimes of validity for each expression are illustrated by calculations on model systems. In addition, the kinetic isotope effects (KIEs) for a series of model PCET reactions are analyzed to elucidate the fundamental physical principles dictating the magnitude of the KIE and the dependence of the KIE on the physical properties of the system, including temperature, reorganization energy, driving force, equilibrium proton donor-acceptor distance, and effective frequency of the proton donor-acceptor mode. These calculations lead to three physical insights that are directly relevant to experimental data. First, these calculations provide an explanation for a decrease in the KIE as the proton donor-acceptor distance increases, even though typically the KIE will increase with increasing equilibrium proton donor-acceptor distance if all other parameters remain fixed. Often the proton donor-acceptor frequency decreases as the proton donor-acceptor distance increases, and these two effects impact the KIE in opposite directions, so either trend could be observed. Second, these calculations provide an explanation for an increase in the KIE as the temperature increases, even though typically the KIE will decrease with increasing temperature if all other parameters remain fixed. The combination of a rigid hydrogen bond, which corresponds to a high proton donor-acceptor frequency, and low solvent polarity, which corresponds to small solvent reorganization energy, allows the KIE to either increase or decrease with temperature, depending on the other properties of the system. Third, these calculations provide insight into the dependence of the rate constant and KIE on the driving force, which has been studied experimentally for a wide range of PCET systems. The rate constant

  18. Compositional differences among Chinese soy sauce types studied by (13)C NMR spectroscopy coupled with multivariate statistical analysis.

    PubMed

    Kamal, Ghulam Mustafa; Wang, Xiaohua; Bin Yuan; Wang, Jie; Sun, Peng; Zhang, Xu; Liu, Maili

    2016-09-01

    Soy sauce a well known seasoning all over the world, especially in Asia, is available in global market in a wide range of types based on its purpose and the processing methods. Its composition varies with respect to the fermentation processes and addition of additives, preservatives and flavor enhancers. A comprehensive (1)H NMR based study regarding the metabonomic variations of soy sauce to differentiate among different types of soy sauce available on the global market has been limited due to the complexity of the mixture. In present study, (13)C NMR spectroscopy coupled with multivariate statistical data analysis like principle component analysis (PCA), and orthogonal partial least square-discriminant analysis (OPLS-DA) was applied to investigate metabonomic variations among different types of soy sauce, namely super light, super dark, red cooking and mushroom soy sauce. The main additives in soy sauce like glutamate, sucrose and glucose were easily distinguished and quantified using (13)C NMR spectroscopy which were otherwise difficult to be assigned and quantified due to serious signal overlaps in (1)H NMR spectra. The significantly higher concentration of sucrose in dark, red cooking and mushroom flavored soy sauce can directly be linked to the addition of caramel in soy sauce. Similarly, significantly higher level of glutamate in super light as compared to super dark and mushroom flavored soy sauce may come from the addition of monosodium glutamate. The study highlights the potentiality of (13)C NMR based metabonomics coupled with multivariate statistical data analysis in differentiating between the types of soy sauce on the basis of level of additives, raw materials and fermentation procedures. PMID:27343582

  19. Dipolar-coupling-mediated total correlation spectroscopy in solid-state 13C NMR: Selection of individual 13C- 13C dipolar interactions

    NASA Astrophysics Data System (ADS)

    Spano, Justin; Wi, Sungsool

    2010-06-01

    Herein is described a useful approach in solid-state NMR, for selecting homonuclear 13C- 13C spin pairs in a multiple- 13C homonuclear dipolar coupled spin system. This method builds upon the zero-quantum (ZQ) dipolar recoupling method introduced by Levitt and coworkers (Marin-Montesinos et al., 2006 [30]) by extending the originally introduced one-dimensional (1D) experiment into a two-dimensional (2D) method with selective irradiation scheme, while moving the 13C- 13C mixing scheme from the transverse to the longitudinal mode, together with a dramatic improvement in the proton decoupling efficiency. Selective spin-pair recoupling experiments incorporating Gaussian and cosine-modulated Gaussian pulses for inverting specific spins were performed, demonstrating the ability to detect informative, simplified/individualized, long-range 13C- 13C homonuclear dipolar coupling interactions more accurately by removing less informative, stronger, short-range 13C- 13C interactions from 2D correlation spectra. The capability of this new approach was demonstrated experimentally on uniformly 13C-labeled Glutamine and a tripeptide sample, GAL.

  20. The Use of Residual Dipolar Coupling in Studying Proteins by NMR

    PubMed Central

    Chen, Kang

    2014-01-01

    The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole–dipole interaction vectors within a common reference frame. Its measurement requires a nonisotropic orientation, through a direct or indirect magnetic field alignment, of the protein in solution. There has been recent progress in the developments of alignment methods to allow the measurement of RDC and of methods to analyze the resulting data. In this chapter we briefly go through the mathematical expressions for the RDC and common descriptions of the alignment tensor, which may be represented using either Saupe order or the principal order matrix. Then we review the latest developments in alignment media. In particular we looked at the lipid-compatible media that allow the measurement of RDCs for membrane proteins. Other methods including conservative surface residue mutation have been invented to obtain up to five orthogonal alignment tensors that provide a potential for de novo structure and dynamics study using RDCs exclusively. We then discuss approximations assumed in RDC interpretations and different views on dynamics uncovered from the RDC method. In addition to routine usage of RDCs in refining a single structure, novel applications such as ensemble refinement against RDCs have been implemented to represent protein structure and dynamics in solution. The RDC application also extends to the study of protein–substrate interaction as well as to solving quaternary structure of oligomer in equilibrium with a monomer, opening an avenue for RDCs in high-order protein structure determination. PMID:21952837

  1. Effect of magnetic field and iron content on NMR proton relaxation of liver, spleen and brain tissues.

    PubMed

    Hocq, Aline; Luhmer, Michel; Saussez, Sven; Louryan, Stéphane; Gillis, Pierre; Gossuin, Yves

    2015-01-01

    Iron accumulation is observed in liver and spleen during hemochromatosis and important neurodegenerative diseases involve iron overload in brain. Storage of iron is ensured by ferritin, which contains a magnetic core. It causes a darkening on T2 -weighted MR images. This work aims at improving the understanding of the NMR relaxation of iron-loaded human tissues, which is necessary to develop protocols of iron content measurements by MRI. Relaxation times measurements on brain, liver and spleen samples were realized at different magnetic fields. Iron content was determined by atomic emission spectroscopy. For all samples, the longitudinal relaxation rate (1/T1 ) of tissue protons decreases with the magnetic field up to 1 T, independently of iron content, while their transverse relaxation rate (1/T2 ) strongly increases with the field, either linearly or quadratically, or a combination thereof. The extent of the inter-echo time dependence of 1/T2 also varies according to the sample. A combination of theoretical models is necessary to describe the relaxation of iron-containing tissues. This can be due to the presence, inside tissues, of ferritin clusters of different sizes and densities. When considering all samples, a correlation (r(2)  = 0.6) between 1/T1 and iron concentration is observed at 7.0 T. In contrast the correlation between 1/T2 and iron content is poor, even at high field (r(2)  = 0.14 at 7.0 T). Our results show that MRI methods based on T1 or T2 measurements will easily detect an iron overloading at high magnetic field, but will not provide an accurate quantification of tissue iron content at low iron concentrations. PMID:24954138

  2. Basic principles of static proton low-resolution spin diffusion NMR in nanophase-separated materials with mobility contrast.

    PubMed

    Schäler, Kerstin; Roos, Matthias; Micke, Peter; Golitsyn, Yury; Seidlitz, Anne; Thurn-Albrecht, Thomas; Schneider, Horst; Hempel, Günter; Saalwächter, Kay

    2015-11-01

    We review basic principles of low-resolution proton NMR spin diffusion experiments, relying on mobility differences in nm-sized phases of inhomogeneous organic materials such as block-co- or semicrystalline polymers. They are of use for estimates of domain sizes and insights into nanometric dynamic inhomogeneities. Experimental procedures and limitations of mobility-based signal decomposition/filtering prior to spin diffusion are addressed on the example of as yet unpublished data on semicrystalline poly(ϵ-caprolactone), PCL. Specifically, we discuss technical aspects of the quantitative, dead-time free detection of rigid-domain signals by aid of the magic-sandwich echo (MSE), and magic-and-polarization-echo (MAPE) and double-quantum (DQ) magnetization filters to select rigid and mobile components, respectively. Such filters are of general use in reliable fitting approaches for phase composition determinations. Spin diffusion studies at low field using benchtop instruments are challenged by rather short (1)H T1 relaxation times, which calls for simulation-based analyses. Applying these, in combination with domain sizes as determined by small-angle X-ray scattering, we have determined spin diffusion coefficients D for PCL (0.34, 0.19 and 0.032nm(2)/ms for crystalline, interphase and amorphous parts, respectively). We further address thermal-history effects related to secondary crystallization. Finally, the state of knowledge concerning the connection between D values determined locally at the atomic level, using (13)C detection and CP- or REDOR-based "(1)H hole burning" procedures, and those obtained by calibration experiments, is summarized. Specifically, the non-trivial dependence of D on the magic-angle spinning (MAS) frequency, with a minimum under static and a local maximum under moderate-MAS conditions, is highlighted. PMID:26404771

  3. Characterization of the Dynamics in the Protonic Conductor CsH2PO4 by 17O Solid-State NMR Spectroscopy and First-Principles Calculations: Correlating Phosphate and Protonic Motion

    PubMed Central

    2015-01-01

    17O NMR spectroscopy combined with first-principles calculations was employed to understand the local structure and dynamics of the phosphate ions and protons in the paraelectric phase of the proton conductor CsH2PO4. For the room-temperature structure, the results confirm that one proton (H1) is localized in an asymmetric H-bond (between O1 donor and O2 acceptor oxygen atoms), whereas the H2 proton undergoes rapid exchange between two sites in a hydrogen bond with a symmetric double potential well at a rate ≥107 Hz. Variable-temperature 17O NMR spectra recorded from 22 to 214 °C were interpreted by considering different models for the rotation of the phosphate anions. At least two distinct rate constants for rotations about four pseudo C3 axes of the phosphate ion were required in order to achieve good agreement with the experimental data. An activation energy of 0.21 ± 0.06 eV was observed for rotation about the P–O1 axis, with a higher activation energy of 0.50 ± 0.07 eV being obtained for rotation about the P–O2, P–O3d, and P–O3a axes, with the superscripts denoting, respectively, dynamic donor and acceptor oxygen atoms of the H-bond. The higher activation energy of the second process is most likely associated with the cost of breaking an O1–H1 bond. The activation energy of this process is slightly lower than that obtained from the 1H exchange process (0.70 ± 0.07 eV) (Kim, G.; Blanc, F.; Hu, Y.-Y.; Grey, C. P. J. Phys. Chem. C2013, 117, 6504−6515) associated with the translational motion of the protons. The relationship between proton jumps and phosphate rotation was analyzed in detail by considering uncorrelated motion, motion of individual PO4 ions and the four connected/H-bonded protons, and concerted motions of adjacent phosphate units, mediated by proton hops. We conclude that, while phosphate rotations aid proton motion, not all phosphate rotations result in proton jumps. PMID:25732257

  4. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Hou, Guangjin; Lu, Xingyu; Vega, Alexander J.; Polenova, Tatyana

    2014-09-01

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear 1H-X (X = 13C, 15N, 31P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the 1H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the 1H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from 1H chemical shift anisotropy, while keeping the 1H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [15N]-N-acetyl-valine and [U-13C,15N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate 1H-15N dipolar couplings in the context of 3D experiments is presented on U-13C,15N-enriched dynein light chain protein LC8.

  5. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

    SciTech Connect

    Hou, Guangjin E-mail: tpolenov@udel.edu; Lu, Xingyu E-mail: lexvega@comcast.net; Vega, Alexander J. E-mail: lexvega@comcast.net; Polenova, Tatyana E-mail: tpolenov@udel.edu

    2014-09-14

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear {sup 1}H-X (X = {sup 13}C, {sup 15}N, {sup 31}P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the {sup 1}H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the {sup 1}H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from {sup 1}H chemical shift anisotropy, while keeping the {sup 1}H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [{sup 15}N]-N-acetyl-valine and [U-{sup 13}C,{sup 15}N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate {sup 1}H-{sup 15}N dipolar couplings in the context of 3D experiments is presented on U-{sup 13}C,{sup 15}N-enriched dynein light chain protein LC8.

  6. A capacitively coupled temperature-jump arrangement for high-resolution biomolecular NMR.

    PubMed

    Gal, Maayan; Zibzener, Koby; Frydman, Lucio

    2010-11-01

    A simple design for performing rapid temperature jumps within a high-resolution nuclear magnetic resonance (NMR) setting is presented and exemplified. The design is based on mounting, around a conventional NMR glass tube, an inductive radiofrequency (RF) irradiation coil that is suitably tuned by a resonant circuit and is driven by one of the NMR's console high-power RF amplifiers. The electric fields generated by this coil's thin metal strips can lead to a fast and efficient heating of the sample, amounting to temperature jumps of ≈ 20 °C in well within a second-particularly in the presence of lossy dielectric media like those provided by physiological buffers. Moreover, when wound around a 4-mm NMR tube, the resulting device fits a conventional 5-mm inverse probe and is wholly compatible with the field homogeneities and sensitivities expected for high-resolution biomolecular NMR conditions. The performance characteristics of this new system were tested using saline solutions, as well as on a lyotropic liquid crystal capable of undergoing nematic → isotropic transitions in the neighborhood of ambient temperature. These settings were then incorporated into the performance of a new kind of single-scan 2D NMR spectroscopy acquisition, correlating the anisotropic and isotropic patterns elicited by solutes dissolved in such liquid-crystalline systems, before and after a sudden temperature jump occurring during an intervening mixing period. PMID:20818777

  7. Proton Quantization and Vibrational Relaxation in Nonadiabatic Dynamics of Photoinduced Proton-Coupled Electron Transfer in a Solvated Phenol-Amine Complex.

    PubMed

    Goyal, Puja; Schwerdtfeger, Christine A; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2016-03-10

    Nonadiabatic dynamics simulations of photoinduced proton-coupled electron transfer (PCET) in a phenol-amine complex in solution were performed. The electronic potential energy surfaces were generated on-the-fly with a hybrid quantum mechanical/molecular mechanical approach that described the solute with a multiconfigurational method in a bath of explicit solvent molecules. The transferring hydrogen nucleus was represented as a quantum mechanical wave function calculated with grid-based methods, and surface hopping trajectories were propagated on the adiabatic electron-proton vibronic surfaces. Following photoexcitation to the excited S1 electronic state, the overall decay to the ground vibronic state was found to be comprised of relatively fast decay from a lower proton vibrational state of S1 to a highly excited proton vibrational state of the ground S0 electronic state, followed by vibrational relaxation within the S0 state. Proton transfer can occur either on the highly excited proton vibrational states of S0 due to small environmental fluctuations that shift the delocalized vibrational wave functions or on the low-energy proton vibrational states of S1 due to solvent reorganization that alters the asymmetry of the proton potential and reduces the proton transfer barrier. The isotope effect arising from replacing the transferring hydrogen with deuterium is predicted to be negligible because hydrogen and deuterium behave similarly in both types of proton transfer processes. Although an isotope effect could be observed for other systems, in general the absence of an isotope effect does not imply the absence of proton transfer in photoinduced PCET systems. This computational approach is applicable to a wide range of other photoinduced PCET processes. PMID:26812149

  8. The possible role of proton-coupled electron transfer (PCET) in water oxidation by photosystem II.

    PubMed

    Meyer, Thomas J; Huynh, My Hang V; Thorp, H Holden

    2007-01-01

    All higher life forms use oxygen and respiration as their primary energy source. The oxygen comes from water by solar-energy conversion in photosynthetic membranes. In green plants, light absorption in photosystem II (PSII) drives electron-transfer activation of the oxygen-evolving complex (OEC). The mechanism of water oxidation by the OEC has long been a subject of great interest to biologists and chemists. With the availability of new molecular-level protein structures from X-ray crystallography and EXAFS, as well as the accumulated results from numerous experiments and theoretical studies, it is possible to suggest how water may be oxidized at the OEC. An integrated sequence of light-driven reactions that exploit coupled electron-proton transfer (EPT) could be the key to water oxidation. When these reactions are combined with long-range proton transfer (by sequential local proton transfers), it may be possible to view the OEC as an intricate structure that is "wired for protons". PMID:17604381

  9. G2A is a proton-sensing G-protein-coupled receptor antagonized by lysophosphatidylcholine.

    PubMed

    Murakami, Naoka; Yokomizo, Takehiko; Okuno, Toshiaki; Shimizu, Takao

    2004-10-01

    G2A (from G2 accumulation) is a G-protein-coupled receptor (GPCR) that regulates the cell cycle, proliferation, oncogenesis, and immunity. G2A shares significant homology with three GPCRs including ovarian cancer GPCR (OGR1/GPR68), GPR4, and T cell death-associated gene 8 (TDAG8). Lysophosphatidylcholine (LPC) and sphingosylphosphorylcholine (SPC) were reported as ligands for G2A and GPR4 and for OGR1 (SPC only), and a glycosphingolipid psychosine was reported as ligand for TDAG8. As OGR1 and GPR4 were reported as proton-sensing GPCRs (Ludwig, M. G., Vanek, M., Guerini, D., Gasser, J. A., Jones, C. E., Junker, U., Hofstetter, H., Wolf, R. M., and Seuwen, K. (2003) Nature 425, 93-98), we evaluated the proton-sensing function of G2A. Transient expression of G2A caused significant activation of the zif 268 promoter and inositol phosphate (IP) accumulation at pH 7.6, and lowering extracellular pH augmented the activation only in G2A-expressing cells. LPC inhibited the pH-dependent activation of G2A in a dose-dependent manner in these assays. Thus, G2A is another proton-sensing GPCR, and LPC functions as an antagonist, not as an agonist, and regulates the proton-dependent activation of G2A. PMID:15280385

  10. Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography

    PubMed Central

    Fukuda, Yohta; Tse, Ka Man; Nakane, Takanori; Nakatsu, Toru; Suzuki, Mamoru; Sugahara, Michihiro; Inoue, Shigeyuki; Masuda, Tetsuya; Yumoto, Fumiaki; Matsugaki, Naohiro; Nango, Eriko; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Song, Changyong; Hatsui, Takaki; Nureki, Osamu; Murphy, Michael E. P.; Inoue, Tsuyoshi; Iwata, So; Mizohata, Eiichi

    2016-01-01

    Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme–substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes. PMID:26929369

  11. Proton coupled electron transfer from the excited state of a ruthenium(II) pyridylimidazole complex.

    PubMed

    Pannwitz, Andrea; Wenger, Oliver S

    2016-04-28

    Proton coupled electron transfer (PCET) from the excited state of [Ru(bpy)2pyimH](2+) (bpy = 2,2'-bipyridine; pyimH = 2-(2'-pyridyl)imidazole) to N-methyl-4,4'-bipyridinium (monoquat, MQ(+)) was studied. While this complex has been investigated previously, our study is the first to show that the formal bond dissociation free energy (BDFE) of the imidazole-N-H bond decreases from (91 ± 1) kcal mol(-1) in the electronic ground state to (43 ± 5) kcal mol(-1) in the lowest-energetic (3)MLCT excited state. This makes the [Ru(bpy)2pyimH](2+) complex a very strong (formal) hydrogen atom donor even when compared to metal hydride complexes, and this is interesting for light-driven (formal) hydrogen atom transfer (HAT) reactions with a variety of different substrates. Mechanistically, formal HAT between (3)MLCT excited [Ru(bpy)2pyimH](2+) and monoquat in buffered 1 : 1 (v : v) CH3CN/H2O was found to occur via a sequence of reaction steps involving electron transfer from Ru(ii) to MQ(+) coupled to release of the N-H proton to buffer base, followed by protonation of reduced MQ(+) by buffer acid. Our study is relevant in the larger contexts of photoredox catalysis and light-to-chemical energy conversion. PMID:27094541

  12. Stoichiometry of Proton Translocation Coupled to Substrate Oxidation in Plant Mitochondria

    PubMed Central

    Moreau, François; de Virville, Jacques Davy

    1985-01-01

    The proton translocation coupled to the electron flux from succinate, exogenous NADH, and NAD+-linked substrates (malate and isocitrate) to cytochrome c and to oxygen was studied in purified potato (Solanum tuberosum) mitochondria using oxygen and ferricyanide pulse techniques. In the presence of valinomycin plus K+ (used as a charge compensating cation), optimum values of H+/2 e− were obtained when low amounts of electron acceptors (oxygen or ferricyanide) were added to the mitochondria (1-2 nanogram [2 e−] equivalents per milligram protein). The stoichiometry of proton translocation to electron flux was unaffected in the presence of N-ethylmaleimide, an inhibitor of the Pi/H+ symport. With succinate as substrate, H+/2 e− ratios were 4.0 ± 0.2 and 3.7 ± 0.3 with oxygen and ferricyanide as electron acceptors, respectively. With exogenous NADH, H+/2e− ratios were 4.1 ± 0.9 and 3.4 ± 0.2, respectively. The proton translocation coupled to the oxidation of NAD+-linked substrates (malate, isocitrate) was dependent upon the presence of adenylates (ADP, AMP, or ATP). For malate (+ glutamate) oxidation the observed H+/2 e− ratios were increased from 3.6 ± 2.2 to 6.5 ± 0.5 in the presence of 20 micromolar ADP. PMID:16663992

  13. Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.

    PubMed

    Fukuda, Yohta; Tse, Ka Man; Nakane, Takanori; Nakatsu, Toru; Suzuki, Mamoru; Sugahara, Michihiro; Inoue, Shigeyuki; Masuda, Tetsuya; Yumoto, Fumiaki; Matsugaki, Naohiro; Nango, Eriko; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Song, Changyong; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Murphy, Michael E P; Inoue, Tsuyoshi; Iwata, So; Mizohata, Eiichi

    2016-03-15

    Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme-substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes. PMID:26929369

  14. Toxicometabolomics approach to urinary biomarkers for mercuric chloride (HgCl{sub 2})-induced nephrotoxicity using proton nuclear magnetic resonance ({sup 1}H NMR) in rats

    SciTech Connect

    Kim, Kyu-Bong; Um, So Young; Chung, Myeon Woo; Jung, Seung Chul; Oh, Ji Seon; Kim, Seon Hwa; Na, Han Sung; Lee, Byung Mu; Choi, Ki Hwan

    2010-12-01

    The primary objective of this study was to determine and characterize surrogate biomarkers that can predict nephrotoxicity induced by mercuric chloride (HgCl{sub 2}) using urinary proton nuclear magnetic resonance ({sup 1}H NMR) spectral data. A procedure for {sup 1}H NMR urinalysis using pattern recognition was proposed to evaluate nephrotoxicity induced by HgCl{sub 2} in Sprague-Dawley rats. HgCl{sub 2} at 0.1 or 0.75 mg/kg was administered intraperitoneally (i.p.), and urine was collected every 24 h for 6 days. Animals (n = 6 per group) were sacrificed 3 or 6 days post-dosing in order to perform clinical blood chemistry tests and histopathologic examinations. Urinary {sup 1}H NMR spectroscopy revealed apparent differential clustering between the control and HgCl{sub 2} treatment groups as evidenced by principal component analysis (PCA) and partial least square (PLS)-discriminant analysis (DA). Time- and dose-dependent separation of HgCl{sub 2}-treated animals from controls was observed by PCA of {sup 1}H NMR spectral data. In HgCl{sub 2}-treated rats, the concentrations of endogenous urinary metabolites of glucose, acetate, alanine, lactate, succinate, and ethanol were significantly increased, whereas the concentrations of 2-oxoglutarate, allantoin, citrate, formate, taurine, and hippurate were significantly decreased. These endogenous metabolites were selected as putative biomarkers for HgCl{sub 2}-induced nephrotoxicity. A dose response was observed in concentrations of lactate, acetate, succinate, and ethanol, where severe disruption of the concentrations of 2-oxoglutarate, citrate, formate, glucose, and taurine was observed at the higher dose (0.75 mg/kg) of HgCl{sub 2}. Correlation of urinary {sup 1}H NMR PLS-DA data with renal histopathologic changes suggests that {sup 1}H NMR urinalysis can be used to predict or screen for HgCl{sub 2}-induced nephrotoxicity{sub .}

  15. α-Substituted Bis(octabutoxyphthalocyaninato)Terbium(III) Double-Decker Complexes: Preparation and Study of Protonation by NMR and DFT.

    PubMed

    Damjanović, Marko; Horie, Yusuke; Morita, Takaumi; Horii, Yoji; Katoh, Keiichi; Yamashita, Masahiro; Enders, Markus

    2015-12-21

    Synthesis of the anionic, α-substituted, bis(phthalocyaninato)Tb(III) complex [Tb(α-obPc)2](-) ([1](-)) (obPc = α-octabutoxyphthalocyaninato) leads to the isolation of its protonated form [1H](0). This complex was characterized by X-ray diffraction (XRD), mass spectroscopy (MS), infrared (IR) and ultraviolet-visible-near-infrared (UV-vis-NIR) spectroscopy. Crystal structure analysis did not allow localization of the additional proton, which is probably attached to the meso-N atom or isoindole-N atom of the phthalocyaninato ligand. [1H](0) can easily be deprotonated or protonated, giving the corresponding anionic and cationic complexes. The three compounds [1H](0), [1](-), and [1HH](+) were studied by a combination of paramagnetic NMR experiments ((1)H, (13)C, variable-temperature measurements, two-dimensional nuclear magnetic resonance and DFT calculations (done on Y(III) analogues with octamethoxyphthalocyaninato ligands), for the purpose of elucidating the positions of the acidic protons and for understanding the structural changes of the coordination environment of the Tb ion induced by protonation. PMID:26650727

  16. A 300 MHz and 600 MHz proton NMR study of a 12 base pair restriction fragment: investigation of structure by relaxation measurements.

    PubMed Central

    Early, T A; Kearns, D R; Hillen, W; Wells, R D

    1980-01-01

    The 1H NMR spectrum of a 12 base pair DNA restriction fragment has been measured at 300 and 600 MHz and resonances from over 70 protons are individually resolved. Relaxation rate measurements have been carried out at 300 MHz and compared with the theoretical predictions obtained using an isotropic rigid rotor model with coordinates derived from a Dreiding model of DNA. The model gives results that are in excellent agreement with experiment for most protons when a 7 nsec rotational correlation time is used, although agreement is improved for certain base protons by using a shorter correlation time for the sugar group, or by increasing the sugar-base interproton distances. A comparison of non-selective and selective spin-lattice relaxation rates for carbon bound protons indicates that there is extensive spin diffusion even in this short DNA fragment. Examination of the spin-spin relaxation rates for the same type of proton on different base pairs reveals little sequence effect on conformation. PMID:6258152

  17. Coupling of electron and proton transport in photosynthetic membranes: molecular mechanism.

    PubMed

    Kukushkin, A; Poltev, S; Khuznetsova, S

    2002-05-15

    Using the method of Modified Neglect of Diatomic Overlap (MNDO), the electronic structure of plastoquinol (PQH(2)) and plastoquinone (PQ) in neutral, singly (PQ(-)) and doubly (PQ(2-)) reduced states is studied. The conformational analysis performed on these molecules shows that in the lowest energy conformation, the angle between the first link of the tail backbone and the ring plane of neutral and singly reduced PQ and plastoquinol is nearly the same and differs by 15 degrees from that of doubly reduced PQ. Nevertheless, for all states of plastoquinone and for plastoquinol, the total energy changes by less than 0.2 eV when the studied angle is varied from 0 degrees to 180 degrees. As in Rhodobacter sphaeroides, the oxygen of the PQ ring is reported to form a hydrogen bond with a nitrogen in the ring of Histidine (His) L 190. The energy of the PQ-His complex was calculated for different redox states of PQ and for several values of the distance between the molecules (N-O distance from 0.2 to 0.5 nm). For every considered complexes, the total energy dependence on the proton position on the line connecting the N and O atoms was determined, to see if the hydrogen bond is formed. It is shown that for only singly reduced PQ this dependence has a symmetric two-well form, i.e. the hydrogen bond is formed. For neutral and doubly reduced PQ, the curve is also two-well but asymmetric, so that the proton is bound to His or to PQ, correspondingly. On the basis of these results, we propose the following scheme of electron-proton coupling. Negatively charged oxygens of PQ form H-bonds with proton donor groups of the surrounding protein and fix PQ in its pocket. While the negative charges of oxygens increase after quinone reduction, protons shift to PQ oxygens and form strong hydrogen bonds with them. Upon second PQ reduction, protons are torn away from surrounding amino acids and form covalent bonds with the quinol. Resulting PQH(2) detaches from its binding place and is

  18. Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins

    PubMed Central

    Whitten, Steven T.; García-Moreno E., Bertrand; Hilser, Vincent J.

    2005-01-01

    Local conformational fluctuations in proteins can affect the coupling between ligand binding and global structural transitions. This finding was established by monitoring quantitatively how the population distribution in the ensemble of microstates of staphylococcal nuclease was affected by proton binding. Analysis of acid unfolding and proton-binding data with an ensemble-based model suggests that local fluctuations: (i) can be effective modulators of ligand-binding affinities, (ii) are important determinants of the cooperativity of ligand-driven global structural transitions, and (iii) are well represented thermodynamically as local unfolding processes. These studies illustrate how an ensemble-based description of proteins can be used to describe quantitatively the interdependence of local conformational fluctuations, ligand-binding processes, and global structural transitions. This level of understanding of the relationship between conformation, energy, and dynamics is required for a detailed mechanistic understanding of allostery, cooperativity, and other complex functional and regulatory properties of macromolecules. PMID:15767576

  19. Absence of Rapid Proton Decay and Origin of Low-Energy Particlesand Yukawa Couplings

    SciTech Connect

    Tatar, Radu; Watari, Taizan

    2006-01-01

    In string theory, massless particles often originate from a symmetry breaking of a large gauge symmetry G to its subgroup H. The absence of dimension-4 proton decay in supersymmetric theories suggests that ({bar D},L) are different from {bar H}({bar 5}) in their origins. In this article, we consider a possibility that they come from different irreducible components in g/h. Requiring that all the Yukawa coupling constants of quarks and leptons be generated from the super Yang-Mills interactions of G, we found in the context of Georgi-Glashow H = SU(5) unification that the minimal choice of G is E{sub 7} and E{sub 8} is the only alternative. This idea is systematically implemented in Heterotic String, M theory and F theory, confirming the absence of dimension 4 proton decay operators. Not only H = SU(5) but also G constrain operators of effective field theories, providing non-trivial information.

  20. Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities.

    PubMed

    Miller, David C; Tarantino, Kyle T; Knowles, Robert R

    2016-06-01

    Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter, we aim to highlight the origins, development, and evolution of the PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups. PMID:27573270

  1. Peptide Selectivity of the Proton-Coupled Oligopeptide Transporter from Neisseria meningitidis.

    PubMed

    Sharma, Neha; Aduri, Nanda G; Iqbal, Anna; Prabhala, Bala K; Mirza, Osman

    2016-01-01

    Peptide transport in living organisms is facilitated by either primary transport, hydrolysis of ATP, or secondary transport, cotransport of protons. In this study, we focused on investigating the ligand specificity of the Neisseria meningitidis proton-coupled oligopeptide transporter (NmPOT). It has been shown that the gene encoding this transporter is upregulated during infection. NmPOT conformed to the typical chain length preference as observed in prototypical transporters of this family. In contrast to prototypical transporters, it was unable to accommodate a positively charged peptide residue at the C-terminus position of the substrate peptide. Sequence analysis of the active site of NmPOT displayed a distinctive aromatic patch, which has not been observed in any other transporters from this family. This aromatic patch may be involved in providing NmPOT with its atypical preferences. This study provides important novel information towards understanding how these transporters recognize their substrates. PMID:27438044

  2. Direct simulation of proton-coupled electron transfer across multiple regimes

    NASA Astrophysics Data System (ADS)

    Kretchmer, Joshua S.; Miller, Thomas F.

    2013-04-01

    The coupled transfer of electrons and protons is a central feature of biological and molecular catalysis, yet fundamental aspects of these reactions remain poorly understood. In this study, we extend the ring polymer molecular dynamics (RPMD) method to enable direct simulation of proton-coupled electron transfer (PCET) reactions across a wide range of physically relevant regimes. In a system-bath model for symmetric, co-linear PCET in the condensed phase, RPMD trajectories reveal distinct kinetic pathways associated with sequential and concerted PCET reaction mechanisms, and it is demonstrated that concerted PCET proceeds by a solvent-gating mechanism in which the reorganization energy is mitigated by charge cancellation among the transferring particles. We further employ RPMD to study the kinetics and mechanistic features of concerted PCET reactions across multiple coupling regimes, including the fully non-adiabatic (both electronically and vibrationally non-adiabatic), partially adiabatic (electronically adiabatic, but vibrationally non-adiabatic), and fully adiabatic (both electronically and vibrationally adiabatic) limits. Comparison of RPMD with the results of PCET rate theories demonstrates the applicability of the direct simulation method over a broad range of conditions; it is particularly notable that RPMD accurately predicts the crossover in the thermal reaction rates between different coupling regimes while avoiding a priori assumptions about the PCET reaction mechanism. Finally, by utilizing the connections between RPMD rate theory and semiclassical instanton theory, we show that analysis of ring-polymer configurations in the RPMD transition path ensemble enables the a posteriori determination of the coupling regime for the PCET reaction. This analysis reveals an intriguing and distinct "transient-proton-bridge" mechanism for concerted PCET that emerges in the transition between the proton-mediated electron superexchange mechanism for fully non

  3. Direct simulation of proton-coupled electron transfer across multiple regimes

    SciTech Connect

    Kretchmer, Joshua S.; Miller, Thomas F. III

    2013-04-07

    The coupled transfer of electrons and protons is a central feature of biological and molecular catalysis, yet fundamental aspects of these reactions remain poorly understood. In this study, we extend the ring polymer molecular dynamics (RPMD) method to enable direct simulation of proton-coupled electron transfer (PCET) reactions across a wide range of physically relevant regimes. In a system-bath model for symmetric, co-linear PCET in the condensed phase, RPMD trajectories reveal distinct kinetic pathways associated with sequential and concerted PCET reaction mechanisms, and it is demonstrated that concerted PCET proceeds by a solvent-gating mechanism in which the reorganization energy is mitigated by charge cancellation among the transferring particles. We further employ RPMD to study the kinetics and mechanistic features of concerted PCET reactions across multiple coupling regimes, including the fully non-adiabatic (both electronically and vibrationally non-adiabatic), partially adiabatic (electronically adiabatic, but vibrationally non-adiabatic), and fully adiabatic (both electronically and vibrationally adiabatic) limits. Comparison of RPMD with the results of PCET rate theories demonstrates the applicability of the direct simulation method over a broad range of conditions; it is particularly notable that RPMD accurately predicts the crossover in the thermal reaction rates between different coupling regimes while avoiding a priori assumptions about the PCET reaction mechanism. Finally, by utilizing the connections between RPMD rate theory and semiclassical instanton theory, we show that analysis of ring-polymer configurations in the RPMD transition path ensemble enables the a posteriori determination of the coupling regime for the PCET reaction. This analysis reveals an intriguing and distinct 'transient-proton-bridge' mechanism for concerted PCET that emerges in the transition between the proton-mediated electron superexchange mechanism for fully non

  4. Correlation between 1H NMR chemical shifts of hydroxyl protons in n-hexanol/cyclohexane and molecular association properties investigated using density functional theory

    NASA Astrophysics Data System (ADS)

    Flores, Mario E.; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

    2016-01-01

    Association of n-hexanol molecules in cyclohexane forming clusters is studied by DFT and 1H NMR. Geometry optimization, corrected binding energies, charge distributions, charge transfer energies, and 1H NMR chemical shifts have been obtained. The calculated chemical shifts of hydroxyl protons have been correlated to experimental data obtained in the range of n-hexanol molar fraction between 0.002 and 0.2, showing that n-hexanol molecules at a molar fraction around 0.1, where well-structured hydrogen bond networks are observed, tend to form linear pentamers and hexamers. The experimental data are consistent with the continuous linear association thermodynamic model, showing a dimensionless association constant of 284.

  5. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis.

    PubMed Central

    Lancaster, C R; Michel, H; Honig, B; Gunner, M R

    1996-01-01

    Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (QB) site, a continuum dielectric model and finite difference technique have been used to identify clusters of electrostatically interacting ionizable residues. Twenty-three residues within a distance of 25 A from QB (QB cluster) have been shown to be strongly electrostatically coupled to QB, either directly or indirectly. An analogous cluster of 24 residues is found to interact with QA (QA cluster). Both clusters extend to the cytoplasmic surface in at least two directions. However, the QB cluster differs from the QA cluster in that it has a surplus of acidic residues, more strong electrostatic interactions, is less solvated, and experiences a strong positive electrostatic field arising from the polypeptide backbone. Consequently, upon reduction of QA or QB, it is the QB cluster, and not the QA cluster, which is responsible for substoichiometric proton uptake at neutral pH. The bulk of the changes in the QB cluster are calculated to be due to the protonation of a tightly coupled cluster of the three Glu residues (L212, H177, and M234) within the QB cluster. If the lifetime of the doubly reduced state QB2- is long enough, Asp M43 and Ser L223 are predicted to also become protonated. The calculated complex titration behavior of the strongly interacting residues of the QB cluster and the resulting electrostatic response to electron transfer may be a common feature in proton-transferring membrane protein complexes. Images FIGURE 2 p2482-a FIGURE 6 FIGURE 8 FIGURE 10 PMID:8744288

  6. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis.

    PubMed

    Lancaster, C R; Michel, H; Honig, B; Gunner, M R

    1996-06-01

    Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (QB) site, a continuum dielectric model and finite difference technique have been used to identify clusters of electrostatically interacting ionizable residues. Twenty-three residues within a distance of 25 A from QB (QB cluster) have been shown to be strongly electrostatically coupled to QB, either directly or indirectly. An analogous cluster of 24 residues is found to interact with QA (QA cluster). Both clusters extend to the cytoplasmic surface in at least two directions. However, the QB cluster differs from the QA cluster in that it has a surplus of acidic residues, more strong electrostatic interactions, is less solvated, and experiences a strong positive electrostatic field arising from the polypeptide backbone. Consequently, upon reduction of QA or QB, it is the QB cluster, and not the QA cluster, which is responsible for substoichiometric proton uptake at neutral pH. The bulk of the changes in the QB cluster are calculated to be due to the protonation of a tightly coupled cluster of the three Glu residues (L212, H177, and M234) within the QB cluster. If the lifetime of the doubly reduced state QB2- is long enough, Asp M43 and Ser L223 are predicted to also become protonated. The calculated complex titration behavior of the strongly interacting residues of the QB cluster and the resulting electrostatic response to electron transfer may be a common feature in proton-transferring membrane protein complexes. PMID:8744288

  7. Measurement of carbon-proton dipolar couplings in liquid crystals using DAPT.

    PubMed

    Jayanthi, S; Madhu, P K; Ramanathan, K V

    2008-11-01

    Dipolar couplings provide valuable information on order and dynamics in liquid crystals. For measuring heteronuclear dipolar couplings in oriented systems, a new separated local field experiment is presented here. The method is based on the dipolar assisted polarization transfer (DAPT) pulse sequence proposed recently (Chem. Phys. Lett. 2007, 439, 407) for transfer of polarization between two spins I and S. DAPT utilizes the evolution of magnetization of the I and S spins under two blocks of phase shifted BLEW-12 pulses on the I spin separated by a 90 degree pulse on the S spin. Compared to the rotating frame techniques based on Hartmann-Hahn match, this approach is easy to implement and is independent of any matching conditions. DAPT can be utilized either as a proton encoded local field (PELF) technique or as a separated local field (SLF) technique, which means that the heteronuclear dipolar coupling can be obtained by following either the evolution of the abundant spin like proton (PELF) or that of the rare spin such as carbon (SLF). We have demonstrated the use of DAPT both as a PELF and as a SLF technique on an oriented liquid crystalline sample at room temperature and also have compared its performance with PISEMA. We have also incorporated modifications to the original DAPT pulse sequence for (i) improving its sensitivity and (ii) removing carrier offset dependence. PMID:18841947

  8. Proton-Coupled Electron Transfer in Molecular Electrocatalysis: Theoretical Methods and Design Principles

    SciTech Connect

    Solis, Brian H.; Hammes-Schiffer, Sharon

    2014-07-07

    Molecular electrocatalysts play an essential role in a wide range of energy conversion processes. The objective of electrocatalyst design is to maximize the turnover frequency and minimize the overpotential for the overall catalytic cycle. Typically the catalytic cycle is dominated by key proton-coupled electron transfer (PCET) processes comprised of sequential or concerted electron transfer and proton transfer steps. A variety of theoretical methods have been developed to investigate the mechanisms, thermodynamics, and kinetics of PCET processes in electrocatalytic cycles. Electronic structure methods can be used to calculate the reduction potentials and pKa’s and to generate thermodynamic schemes, free energy reaction pathways, and Pourbaix diagrams, which indicate the most stable species at each pH and potential. These types of calculations have assisted in identifying the thermodynamically favorable mechanisms under specified experimental conditions, such as acid strength and overpotential. Such calculations have also revealed linear correlations among the thermodynamic properties, which can be used to predict the impact of modifying the ligand, substituents, or metal center. The role of non-innocent ligands, namely ligand protonation or reduction, has also been examined theoretically. In addition, the rate constants for electron and proton transfer reactions, as well as concerted PCET reactions, have been calculated to investigate the kinetics of molecular electrocatalysts. The concerted PCET mechanism is thought to lower the overpotential required for catalysis by avoiding high-energy intermediates. Rate constant calculations have revealed that the concerted mechanism involving intramolecular proton transfer will be favored by designing more flexible ligands that facilitate the proton donor-acceptor motion while also maintaining a sufficiently short equilibrium proton donor-acceptor distance. Overall, theoretical methods have assisted in the interpretation

  9. Nonadiabatic dynamics of photoinduced proton-coupled electron transfer: comparison of explicit and implicit solvent simulations.

    PubMed

    Auer, Benjamin; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2012-07-01

    Theoretical approaches for simulating the ultrafast dynamics of photoinduced proton-coupled electron transfer (PCET) reactions in solution are developed and applied to a series of model systems. These processes are simulated by propagating nonadiabatic surface hopping trajectories on electron-proton vibronic surfaces that depend on the solute and solvent nuclear coordinates. The PCET system is represented by a four-state empirical valence bond model, and the solvent is treated either as explicit solvent molecules or as a dielectric continuum, in which case the solvent dynamics is described in terms of two collective solvent coordinates corresponding to the energy gaps associated with electron and proton transfer. The explicit solvent simulations reveal two distinct solvent relaxation time scales, where the faster time scale relaxation corresponds to librational motions of solvent molecules in the first solvation shell, and the slower time scale relaxation corresponds to the bulk solvent dielectric response. The charge transfer dynamics is strongly coupled to both the fast and slow time scale solvent dynamics. The dynamical multistate continuum theory is extended to include the effects of two solvent relaxation time scales, and the resulting coupled generalized Langevin equations depend on parameters that can be extracted from equilibrium molecular dynamics simulations. The implicit and explicit solvent approaches lead to qualitatively similar charge transfer and solvent dynamics for model PCET systems, suggesting that the implicit solvent treatment captures the essential elements of the nonequilibrium solvent dynamics for many systems. A combination of implicit and explicit solvent approaches will enable the investigation of photoinduced PCET processes in a variety of condensed phase systems. PMID:22651684

  10. No-D NMR (no-deuterium proton NMR) spectroscopy: a simple yet powerful method for analyzing reaction and reagent solutions.

    PubMed

    Hoye, Thomas R; Eklov, Brian M; Ryba, Troy D; Voloshin, Mikhail; Yao, Letitia J

    2004-03-18

    [reaction: see text] The title technique is a convenient and powerful method for directly monitoring or assaying any reaction mixture or reagent solution. Examples of some common processes (Fischer esterification, lithiation, butyllithium/THF compatibility, olefin metathesis, and a quantification assay), each interrogated in its native solvent, are presented. The spectral data are easy to acquire, and the information content makes a compelling case for routine use of No-D NMR spectroscopy. PMID:15012073

  11. Spin-spin coupling in the HD molecule determined from 1H and 2H NMR experiments in the gas-phase

    NASA Astrophysics Data System (ADS)

    Garbacz, Piotr

    2014-10-01

    The indirect spin-spin coupling of hydrogen deuteride, J(D, H), was determined from a series of 1H and 2H NMR spectra acquired at various densities of gaseous solvents (He, Ar, CO2, and N2O). The analysis of these spectra shows that accurate determination of J(D, H) from this experimental data requires careful examination of the effects of nuclear relaxation and of HD-solvent gas interactions on hydrogen deuteride line shapes. Particularly, it was found that the first-order corrections of the peak-to-peak separations between HD multiplet peaks due to weak van der Waals interactions are proportional to solvent gas density, while these corrections for nuclear relaxation of the proton and the deuteron are proportional to the second power of the inverse of the gas density. Analysis of the data indicates that J(D, H), obtained by correcting for the effects of nuclear relaxation and intermolecular interactions, is 43.136(7) Hz at 300 K.

  12. Uptake of metal ions by a new chelating ion exchange resin. Part 3: Protonation constants via potentiometric titration and solid state [sup 31]P NMR spectroscopy

    SciTech Connect

    Nash, K.L.; Rickert, P.G.; Muntean, J.V.; Alexandratos, S.D.

    1994-01-01

    A new chelating ion exchange resin which incorporates methylenediphosphonate, carboxylate, and sulfonate functional groups in a polystyrene-divinylbenzene matrix has been prepared. This resin exhibits exceptionally high affinity for polyvalent cations even from moderately acidic aqueous media. Metal ion coordination occurs primarily at the diphosphonate group with the secondary binding sites contributing to charge neutralization when necessary and possible, and to increasing hydrophilicity of the resin pores. In the present investigation, the protonation equilibria of the phosphonate groups in the resin are investigated via potentiometric titration and solid-state [sup 31]P NMR spectroscopy of the resin. Intrinsic equilibrium constants for the first two diphosphonate protonation reactions are pK[sub 4] = 10.47 and pK[sub 3] = 7.24. The last two protons added to the diphosphonate group are acidic having pK[sub a] values less than 2.5. These protonation constants are consistent with those reported previously for monomer analog 1,1-diphosphonic acids. This result implies that thermodynamic data available in the literature can be used to predict the relative affinity of the resin for polyvalent cations. 17 refs., 2 figs., 3 tabs.

  13. Peroxyl Radical Reactions in Water Solution: A Gym for Proton-Coupled Electron-Transfer Theories.

    PubMed

    Amorati, Riccardo; Baschieri, Andrea; Morroni, Gloria; Gambino, Rossana; Valgimigli, Luca

    2016-06-01

    The reactions of alkylperoxyl radicals with phenols have remained difficult to investigate in water. We describe herein a simple and reliable method based on the inhibited autoxidation of water/THF mixtures, which we calibrated against pulse radiolysis. With this method we measured the rate constants kinh for the reactions of 2-tetrahydrofuranylperoxyl radicals with reference compounds: urate, ascorbate, ferrocenes, 2,2,5,7,8-pentamethyl-6-chromanol, Trolox, 6-hydroxy-2,5,7,8-tetramethylchroman-2-acetic acid, 2,6-di-tert-butyl-4-methoxyphenol, 4-methoxyphenol, catechol and 3,5-di-tert-butylcatechol. The role of pH was investigated: the value of kinh for Trolox and 4-methoxyphenol increased 11- and 50-fold from pH 2.1 to 12, respectively, which indicate the occurrence of a SPLET-like mechanism. H(D) kinetic isotope effects combined with pH and solvent effects suggest that different types of proton-coupled electron transfer (PCET) mechanisms are involved in water: less electron-rich phenols react at low pH by concerted electron-proton transfer (EPT) to the peroxyl radical, whereas more electron-rich phenols and phenoxide anions react by multi-site EPT in which water acts as proton relay. PMID:27111024

  14. Exogenous control over intracellular acidification: Enhancement via proton caged compounds coupled to gold nanoparticles.

    PubMed

    Carbone, Marilena; Sabbatella, Gianfranco; Antonaroli, Simonetta; Remita, Hynd; Orlando, Viviana; Biagioni, Stefano; Nucara, Alessandro

    2015-11-01

    The pH regulation has a fundamental role in several intracellular processes and its variation via exogenous compounds is a potential tool for intervening in the intracellular processes. Proton caged compounds (PPCs) release protons upon UV irradiation and may efficiently provoke intracellular on-command acidification. Here, we explore the intracellular pH variation, when purposely synthesized PCCs are coupled to gold nanoparticles (AuNPs) and dosed to HEK-293 cells. We detected the acidification process caused by the UV irradiation by monitoring the intensity of the asymmetric stretching mode of the CO(2) molecule at 2343 cm(-1). The comparison between free and AuNPs functionalized proton caged compound demonstrates a highly enhanced CO(2) yield, hence pH variation, in the latter case. Finally, PCC functionalized AuNPs were marked with a purposely synthesized fluorescent marker and dosed to HEK-293 cells. The corresponding fluorescence optical images show green grains throughout the whole cytoplasm. PMID:26235337

  15. Proton Coupled Electron Transfer Reactions at the Surface of Metal Oxide Nanomaterials

    NASA Astrophysics Data System (ADS)

    Braten, Miles N.

    Nanostructured metal oxide materials are found in many products and processes in our society today, but they play a particularly important role in the conversion and storage of energy. The materials are used as catalysts and redox active supports in devices such as dye sensitized solar cells, solid oxide fuel cells, and flow batteries, where they transfer and store electrons and charge balancing cations. Oftentimes electron transfer is modulated by the cations and when the cation is a proton, these redox reactions are known as proton coupled electron transfer (PCET) reactions. The work described in this dissertation focuses on understanding the PCET reactivity of nanocrystalline metal oxide materials. Chapter 1 introduces the concept of PCET and provides background information on the zinc oxide (ZnO) nanocrystals (NCs) which the majority of the research is focused on. Chapter 2 examines the chemistry that occurs during the photoreduction of ZnO NCs. Chapter 3 describes experiments probing how ZnO NC capping ligand concentration and NC size modulate PCET reaction rates. Chapter 4 describes experiments that compare the PCET reactivity of ZnO NCs with different numbers of electrons and protons stored on them. Chapter 5 describes attempts to observe the electrochemical reduction of ZnO NCs attached to gold electrodes. Finally, Chapter 6 contains attempts to identify a nanostructured metal oxide alkane oxidation catalyst for use in fuel cell.

  16. Theory of proton-coupled electron transfer in energy conversion processes.

    PubMed

    Hammes-Schiffer, Sharon

    2009-12-21

    Proton-coupled electron transfer (PCET) reactions play an essential role in a broad range of energy conversion processes, including photosynthesis and respiration. These reactions also form the basis of many types of solar fuel cells and electrochemical devices. Recent advances in the theory of PCET enable the prediction of the impact of system properties on the reaction rates. These predictions may guide the design of more efficient catalysts for energy production, including those based on artificial photosynthesis and solar energy conversion. This Account summarizes the theoretically predicted dependence of PCET rates on system properties and illustrates potential approaches for tuning the reaction rates in chemical systems. A general theoretical formulation for PCET reactions has been developed over the past decade. In this theory, PCET reactions are described in terms of nonadiabatic transitions between the reactant and product electron-proton vibronic states. A series of nonadiabatic rate constant expressions for both homogeneous and electrochemical PCET reactions have been derived in various well-defined limits. Recently this theory has been extended to include the effects of solvent dynamics and to describe ultrafast interfacial PCET. Analysis of the rate constant expressions provides insight into the underlying physical principles of PCET and enables the prediction of the dependence of the rates on the physical properties of the system. Moreover, the kinetic isotope effect, which is the ratio of the rates for hydrogen and deuterium, provides a useful mechanistic probe. Typically the PCET rate will increase as the electronic coupling and temperature increase and as the total reorganization energy and equilibrium proton donor-acceptor distance decrease. The rate constant is predicted to increase as the driving force becomes more negative, rather than exhibit turnover behavior in the inverted region, because excited vibronic product states associated with low

  17. Direct simulation of proton-coupled electron transfer reaction dynamics and mechanisms

    NASA Astrophysics Data System (ADS)

    Kretchmer, Joshua S.; Miller, Thomas F., III

    2014-03-01

    Proton-coupled electron transfer (PCET) reactions, in which both an electron and an associated proton undergo reactive transfer, play an important role in many chemical and biological systems. Due to the complexity of this class of reactions, a variety of different mechanisms fall under the umbrella of PCET. However, the physical driving forces that determine the preferred mechanism in a given system still remain poorly understood. Towards this end, we extend ring polymer molecular dynamics (RPMD), a path-integral quantum dynamics method, to enable the direct simulation and characterization of PCET reaction dynamics in both fully atomistic and system-bath models of organometallic catalysts. In addition to providing validation for the simulation method via extensive comparison with existing PCET rate theories, we analyze the RPMD trajectories to investigate the competition between the concerted and sequential reaction mechanisms for PCET, elucidating the large role of the solvent in controlling the preferred mechanism. We further employ RPMD to determine the kinetics and mechanistic features of concerted PCET reactions across different regimes of electronic and vibrational coupling, providing evidence for a new and distinct PCET reaction mechanism.

  18. Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine.

    PubMed

    Sychrovský, Vladimír; Sponer, Jirí; Hobza, Pavel

    2004-01-21

    The calculated intermolecular and intramolecular indirect NMR spin-spin coupling constants and NMR shifts were used for the discrimination between the inner-shell and the outer-shell binding motif of hydrated divalent cations Mg(2+) or Zn(2+) with a guanine base. The intermolecular coupling constants (1)J(X,O6) and (1)J(X,N7) (X = Mg(2+), Zn(2+)) can be unambiguously assigned to the specific inner-shell binding motif of the hydrated cation either with oxygen O6 or with nitrogen N7 of guanine. The calculated coupling constants (1)J(Mg,O6) and (1)J(Zn,O6) were 6.2 and -17.5 Hz, respectively, for the inner-shell complex of cation directly interacting with oxygen O6 of guanine. For the inner-shell coordination of the cation at nitrogen N7, the calculated coupling constants (1)J(Mg,N7) and (1)J(Zn,N7) were 5.6 and -36.5 Hz, respectively. When the binding of the cation is water-mediated, the coupling constant is zero. To obtain reliable shifts in NMR parameters, hydrated guanine was utilized as the reference state. The calculated change of NMR spin-spin coupling constants due to the hydration and coordination of the cation with guanine is caused mainly by the variation of Fermi-contact coupling contribution while the variation of diamagnetic spin-orbit, paramagnetic spin-orbit, and spin-dipolar coupling contributions is small. The change of s-character of guanine sigma bonding, sigma antibonding, and lone pair orbitals upon the hydration and cation coordination (calculated using the Natural Bond Orbital analysis) correlates with the variation of the Fermi-contact term. The calculated NMR shifts delta(N7) of -15.3 and -12.2 ppm upon the coordination of Mg(2+) and Zn(2+) ion are similar to the NMR shift of 19.6 ppm toward the high field measured by Tanaka for N7 of guanine upon the coordination of the Cd(2+) cation (Tanaka, Y.; Kojima, C.; Morita, E. H.; Kasai. Y.; Yamasaki, K.; Ono, A.; Kainosho, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 4595-4601). The present data

  19. Structural characterization of chemical warfare agent degradation products in decontamination solutions with proton band-selective (1)H-(31)P NMR spectroscopy.

    PubMed

    Koskela, Harri; Hakala, Ullastiina; Vanninen, Paula

    2010-06-15

    Decontamination solutions, which are usually composed of strong alkaline chemicals, are used for efficient detoxification of chemical warfare agents (CWAs). The analysis of CWA degradation products directly in decontamination solutions is challenging due to the nature of the matrix. Furthermore, occasionally an unforeseen degradation pathway can result in degradation products which could be eluded to in standard analyses. Here, we present the results of the application of proton band-selective (1)H-(31)P NMR spectroscopy, i.e., band-selective 1D (1)H-(31)P heteronuclear single quantum coherence (HSQC) and band-selective 2D (1)H-(31)P HSQC-total correlation spectroscopy (TOCSY), for ester side chain characterization of organophosphorus nerve agent degradation products in decontamination solutions. The viability of the approach is demonstrated with a test mixture of typical degradation products of nerve agents sarin, soman, and VX. The proton band-selective (1)H-(31)P NMR spectroscopy is also applied in characterization of unusual degradation products of VX in GDS 2000 solution. PMID:20507069

  20. Exogenous control over intracellular acidification: Enhancement via proton caged compounds coupled to gold nanoparticles and an alternative pathway with DMSO

    PubMed Central

    Carbone, Marilena; Sabbatella, Gianfranco; Antonaroli, Simonetta; Remita, Hynd; Orlando, Viviana; Biagioni, Stefano; Nucara, Alessandro

    2016-01-01

    Proton caged compounds exhibit a characteristic behavior when directly dosed into cells or being coupled to gold nanoparticles prior to the dosing. When irradiated in the near ultraviolet region, they release protons that interact with intracellular HCO3− to yield H2CO3. The dissociation of carbonic acid, then, releases CO2 that can be distinctively singled out in infrared spectra. In the process of searching a pathway to augment the intracellular uptake of proton caged compounds, we probed the association of 1-(2-nitrophenyl)-ethylhexadecyl sulfonate (HDNS) with DMSO, an agent to enhance the membrane permeability. We found out a different UV-induced protonation mechanism that opens up to new conduits of employing of proton caged compounds. Here, we report the infrared data we collected in this set of experiments. PMID:26870760

  1. Exogenous control over intracellular acidification: Enhancement via proton caged compounds coupled to gold nanoparticles and an alternative pathway with DMSO.

    PubMed

    Carbone, Marilena; Sabbatella, Gianfranco; Antonaroli, Simonetta; Remita, Hynd; Orlando, Viviana; Biagioni, Stefano; Nucara, Alessandro

    2016-03-01

    Proton caged compounds exhibit a characteristic behavior when directly dosed into cells or being coupled to gold nanoparticles prior to the dosing. When irradiated in the near ultraviolet region, they release protons that interact with intracellular HCO3 (-) to yield H2CO3. The dissociation of carbonic acid, then, releases CO2 that can be distinctively singled out in infrared spectra. In the process of searching a pathway to augment the intracellular uptake of proton caged compounds, we probed the association of 1-(2-nitrophenyl)-ethylhexadecyl sulfonate (HDNS) with DMSO, an agent to enhance the membrane permeability. We found out a different UV-induced protonation mechanism that opens up to new conduits of employing of proton caged compounds. Here, we report the infrared data we collected in this set of experiments. PMID:26870760

  2. Hydrogen Bonding Networks Tune Proton-Coupled Redox Steps during the Enzymatic Six-Electron Conversion of Nitrite to Ammonia

    PubMed Central

    2015-01-01

    Multielectron multiproton reactions play an important role in both biological systems and chemical reactions involved in energy storage and manipulation. A key strategy employed by nature in achieving such complex chemistry is the use of proton-coupled redox steps. Cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron seven-proton reduction of nitrite to ammonia. While a catalytic mechanism for ccNiR has been proposed on the basis of studies combining computation and crystallography, there have been few studies directly addressing the nature of the proton-coupled events that are predicted to occur along the nitrite reduction pathway. Here we use protein film voltammetry to directly interrogate the proton-coupled steps that occur during nitrite reduction by ccNiR. We find that conversion of nitrite to ammonia by ccNiR adsorbed to graphite electrodes is defined by two distinct phases; one is proton-coupled, and the other is not. Mutation of key active site residues (H257, R103, and Y206) modulates these phases and specifically alters the properties of the detected proton-dependent step but does not inhibit the ability of ccNiR to conduct the full reduction of nitrite to ammonia. We conclude that the active site residues examined are responsible for tuning the protonation steps that occur during catalysis, likely through an extensive hydrogen bonding network, but are not necessarily required for the reaction to proceed. These results provide important insight into how enzymes can specifically tune proton- and electron transfer steps to achieve high turnover numbers in a physiological pH range. PMID:25137350

  3. Binding of oxytocin and 8-arginine-vasopressin to neurophysin studied by /sup 15/N NMR using magnetization transfer and indirect detection via protons

    SciTech Connect

    Live, D.H.; Cowburn, D.

    1987-10-06

    NMR was used to monitor the binding to neurophysin of oxytocin and 8-arginine-vasopressin, /sup 15/N labeling being used to identify specific backbone /sup 15/N and /sup 1/H signals. The most significant effects of binding were large downfield shifts in the amino nitrogen resonance of Phe-3 of vasopressin and in its associated proton, providing evidence that the peptide bond between residues 2 and 3 of the hormones is hydrogen-bonded to the protein within hormone-neurophysin complexes. Suggestive evidence for hydrogen bonding of the amino nitrogen of Tyr-2 was also obtained in the form of decreased proton exchange rates on binding; however, the chemical shift changes of this nitrogen and its associated proton indicated that such hydrogen bonding, if present, is probably weak. Shifts in the amino nitrogen of Asn-5 and in the -NH protons of both Asn-5 and Cys-6 demonstrated that these residues are significantly perturbed by binding, suggesting conformational changes of the ring on binding and/or the presence of binding sites on the hormone outside the 1-3 region. No support was obtained for the thesis that there is a significant second binding site for vasopressin on each neutrophysin chain. The behavior of both oxytocin and vasopressin on binding was consistent with formation of 1:1 complexes in slow exchange with the free state under most pH conditions. At low pH there was evidence of an increased exchange rate. Additionally, broadening of /sup 15/N resonances in the bound state at low pH occurred without a corresponding change in the resonances of equilibrating free hormone. The results suggest significant conformational alteration in neurophysin-hormone complexes at low pH possibly associated with protonation of the carboxyl group of the hormone-protein salt bridge.

  4. TDAG8 is a proton-sensing and psychosine-sensitive G-protein-coupled receptor.

    PubMed

    Wang, Ju-Qiang; Kon, Junko; Mogi, Chihiro; Tobo, Masayuki; Damirin, Alatangaole; Sato, Koichi; Komachi, Mayumi; Malchinkhuu, Enkhzol; Murata, Naoya; Kimura, Takao; Kuwabara, Atsushi; Wakamatsu, Kaori; Koizumi, Hideki; Uede, Toshimitsu; Tsujimoto, Gozoh; Kurose, Hitoshi; Sato, Takashi; Harada, Akihiro; Misawa, Norihiko; Tomura, Hideaki; Okajima, Fumikazu

    2004-10-29

    T cell death-associated gene 8 (TDAG8) has been reported to be a receptor for psychosine. Ovarian cancer G-protein-coupled receptor 1 (OGR1) and GPR4, G-protein-coupled receptors (GPCRs) closely related to TDAG8, however, have recently been identified as proton-sensing or extracellular pH-responsive GPCRs that stimulate inositol phosphate and cAMP production, respectively. In the present study, we examined whether TDAG8 senses extracellular pH change. In the several cell types that were transfected with TDAG8 cDNA, cAMP was markedly accumulated in response to neutral to acidic extracellular pH, with a peak response at approximately pH 7.0-6.5. The pH effect was inhibited by copper ions and was reduced or lost in cells expressing mutated TDAG8 in which histidine residues were changed to phenylalanine. In the membrane fractions prepared from TDAG8-transfected cells, guanosine 5'-O-(3-thiotriphosphate) binding activity and adenylyl cyclase activity were remarkably stimulated in response to neutral and acidic pH. The concentration-dependent effect of extracellular protons on cAMP accumulation was shifted to the right in the presence of psychosine. The inhibitory psychosine effect was also observed for pH-dependent actions in OGR1- and GPR4-expressing cells but not for prostaglandin E(2)- and sphingosine 1-phosphate-induced actions in any pH in native and sphingosine 1-phosphate receptor-expressing cells. Glucosylsphingosine and sphingosylphosphorylcholine similarly inhibited the pH-dependent action, although to a lesser extent. Psychosine-sensitive and pH-dependent cAMP accumulation was also observed in mouse thymocytes. We concluded that TDAG8 is one of the proton-sensing GPCRs coupling to adenylyl cyclase and psychosine, and its related lysosphingolipids behave as if they were antagonists against protein-sensing receptors, including TDAG8, GPR4, and OGR1. PMID:15326175

  5. Assignment of selected hyperfine proton NMR resonances in the met forms of Glycera dibranchiata monomer hemoglobins and comparisons with sperm whale metmyoglobin

    SciTech Connect

    Constantinidis, I.; Satterlee, J.D.; Pandey, R.K.; Leung, H.K.; Smith, K.M.

    1988-04-19

    This work indicates a high degree of purity for our preparations of all three of the primary Glycera dibranchiata monomer hemoglobins and details assignments of the heme methyl and vinyl protons in the hyperfine shift region of the ferric (aquo.) protein forms. The assignments were carried out by reconstituting the apoproteins of each component with selectively deuteriated hemes. The results indicate that even though the individual component preparations consist of essentially a single protein, the proton NMR spectra indicate spectroscopic heterogeneity. Evidence is presented for identification and classification of major and minor protein forms that are present in solutions of each component. Finally, in contrast to previous results, a detailed analysis of the proton hyperfine shift patterns of the major and minor forms of each component, in comparison to the major and minor forms of metmyoglobin, leads to the conclusions that the corresponding forms of the proteins from each species have strikingly similar heme-globin contacts and display nearly identical heme electronic structures and coordination numbers.

  6. Bulk magnetization and 1H NMR spectra of magnetically heterogeneous model systems

    SciTech Connect

    Levin, E M; Bud' ko, S L

    2011-04-28

    Bulk magnetization and ¹H static and magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of two magnetically heterogeneous model systems based on laponite (LAP) layered silicate or polystyrene (PS) with low and high proton concentration, respectively, and ferrimagnetic Fe₂O₃ nano- or micro-particles have been studied. In LAP+Fe₂O₃, a major contribution to the NMR signal broadening is due to the dipolar coupling between the magnetic moments of protons and magnetic particles. In PS+Fe₂O₃, due to the higher proton concentration in polystyrene and stronger proton–proton dipolar coupling, an additional broadening is observed, i.e. ¹H MAS NMR spectra of magnetically heterogeneous systems are sensitive to both proton–magnetic particles and proton–proton dipolar couplings. An increase of the volume magnetization by ~1 emu/cm³ affects the ¹H NMR signal width in a way that is similar to an increase of the proton concentration by ~2×10²²/cm³. ¹H MAS NMR spectra, along with bulk magnetization measurements, allow the accurate determination of the hydrogen concentration in magnetically heterogeneous systems.

  7. Electronic Structure, NMR, Spin-Spin Coupling, and Noncovalent Interactions in Aromatic Amino Acid Based Ionic Liquids.

    PubMed

    Rao, Soniya S; Gejji, Shridhar P

    2016-07-21

    Noncovalent interactions accompanying phenylalanine (Phe), tryptophan (Trp), and tyrosine (Tyr) amino acids based ionic liquids (AAILs) composed of 1-methyl-3-butyl-imidazole and its methyl-substituted derivative as cations have been analyzed employing the dispersion corrected density functional theory. It has been shown that cation-anion binding in these bioionic ILs is primarily facilitated through hydrogen bonding in addition to lp---π and CH---π interactions those arising from aromatic moieties which can be probed through (1)H and (13)C NMR spectra calculated from the gauge independent atomic orbital method. Characteristic NMR spin-spin coupling constants across hydrogen bonds of ion pair structures viz., Fermi contact, spin-orbit and spin-dipole terms show strong dependence on mutual orientation of cation with the amino acid anion. The spin-spin coupling mechanism transmits spin polarization via electric field effect originating from lp---π interactions whereas the electron delocalization from lone pair on the carbonyl oxygen to antibonding C-H orbital is facilitated by hydrogen bonding. It has been demonstrated that indirect spin-spin coupling constants across the hydrogen bonds correlate linearly with hydrogen bond distances. The binding energies and dissected nucleus independent chemical shifts (NICS) document mutual reduction of aromaticity of hydrogen bonded ion pairs consequent to localization of π-character. Moreover the nature and type of such noncovalent interactions governing the in-plane and out-of-plane NICS components provide a measure of diatropic and paratropic currents for the aromatic rings of varying size in AAILs. Besides the direction of frequency shifts of characteristic C═O and NH stretching vibrations in the calculated vibrational spectra has been rationalized. PMID:27336283

  8. Electron/proton coupling in bacterial nitric oxide reductase during reduction of oxygen.

    PubMed

    Flock, Ulrika; Watmough, Nicholas J; Adelroth, Pia

    2005-08-01

    The respiratory nitric oxide reductase (NOR) from Paracoccus denitrificans catalyzes the two-electron reduction of NO to N(2)O (2NO + 2H(+) + 2e(-) --> N(2)O + H(2)O), which is an obligatory step in the sequential reduction of nitrate to dinitrogen known as denitrification. NOR has four redox-active cofactors, namely, two low-spin hemes c and b, one high-spin heme b(3), and a non-heme iron Fe(B), and belongs to same superfamily as the oxygen-reducing heme-copper oxidases. NOR can also use oxygen as an electron acceptor; this catalytic activity was investigated in this study. We show that the product in the steady-state reduction of oxygen is water. A single turnover of the fully reduced NOR with oxygen was initiated using the flow-flash technique, and the progress of the reaction monitored by time-resolved optical absorption spectroscopy. Two major phases with time constants of 40 micros and 25 ms (pH 7.5, 1 mM O(2)) were observed. The rate constant for the faster process was dependent on the O(2) concentration and is assigned to O(2) binding to heme b(3) at a bimolecular rate constant of 2 x 10(7) M(-)(1) s(-)(1). The second phase (tau = 25 ms) involves oxidation of the low-spin hemes b and c, and is coupled to the uptake of protons from the bulk solution. The rate constant for this phase shows a pH dependence consistent with rate limitation by proton transfer from an internal group with a pK(a) = 6.6. This group is presumably an amino acid residue that is crucial for proton transfer to the catalytic site also during NO reduction. PMID:16060680

  9. Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation.

    PubMed

    Gill, Michelle L; Palmer, Arthur G

    2014-09-25

    The present work demonstrates that NMR spin relaxation rate constants for molecules interconverting between states with different diffusion tensors can be modeled theoretically by combining orientational correlation functions for exchanging spherical molecules with locally isotropic approximations for the diffusion anisotropic tensors. The resulting expressions are validated by comparison with correlation functions obtained by Monte Carlo simulations and are accurate for moderate degrees of diffusion anisotropy typically encountered in investigations of globular proteins. The results are complementary to an elegant, but more complex, formalism that is accurate for all degrees of diffusion anisotropy [Ryabov, Y.; Clore, G. M.; Schwieters, C. D. J. Chem. Phys. 2012, 136, 034108]. PMID:25167331

  10. Proton-coupled electron transfer at modified electrodes by multiple pathways.

    PubMed

    Chen, Zuofeng; Vannucci, Aaron K; Concepcion, Javier J; Jurss, Jonah W; Meyer, Thomas J

    2011-12-27

    In single site water or hydrocarbon oxidation catalysis with polypyridyl Ru complexes such as [Ru(II)(Mebimpy)(bpy)(H(2)O)](2+) [where bpy is 2,2'-bipyridine, and Mebimpy is 2,6-bis(1-methylbenzimidazol-2-yl)pyridine] 2, or its surface-bound analog [Ru(II)(Mebimpy)(4,4'-bis-methlylenephosphonato-2,2'-bipyridine)(OH(2))](2+) 2-PO(3)H(2), accessing the reactive states, Ru(V) = O(3+)/Ru(IV) = O(2+), at the electrode interface is typically rate limiting. The higher oxidation states are accessible by proton-coupled electron transfer oxidation of aqua precursors, but access at inert electrodes is kinetically inhibited. The inhibition arises from stepwise mechanisms which impose high energy barriers for 1e- intermediates. Oxidation of the Ru(III)-OH(2+) or forms of 2-PO(3)H(2) to Ru(IV) = O(2+) on planar fluoride-doped SnO(2) electrode and in nanostructured films of Sn(IV)-doped In(2)O(3) and TiO(2) has been investigated with a focus on identifying microscopic phenomena. The results provide direct evidence for important roles for the nature of the electrode, temperature, surface coverage, added buffer base, pH, solvent, and solvent H(2)O/D(2)O isotope effects. In the nonaqueous solvent, propylene carbonate, there is evidence for a role for surface-bound phosphonate groups as proton acceptors. PMID:22160681

  11. Ionosphere-exosphere coupling through charge exchange and momentum transfer in hydrogen-proton collisions

    NASA Technical Reports Server (NTRS)

    Hodges, R. R., Jr.; Breig, E. L.

    1991-01-01

    The implications of a traditional assumption of exospheric physics, that collisions of hydrogen atoms and protons preferentially result in charge exchange with negligible momentum transfer are examined. Initially adopted as a necessary convenience to accommodate limited computer resources in exosphere model calculations, this approximation results in a direct transformation of the proton velocity distribution into a hot component of neutral hydrogen. With expanding computational facilities, the need for the approximation has passed. As the first step toward its replacement with a realistic, quantum mechanical model of the H - H(+) collision process, differential and cumulative cross sections were calculated for quantum elastic scattering of indistinguishable nuclei for a fine grid of encounter energies and scattering angles. These data are used to study the nature of ionosphere-exosphere coupling through H - H(+) collisions, and to demonstrate that the distribution of velocities of scattered H produced in the traditional exospheric charge exchange approximation, as well as that arising from an alternative, fluid dynamic approach, leads to unacceptable abundances of coronal atoms in long-term, highly elliptic trajectories.

  12. Coupling factor B is a component of the Fo proton channel of mitochondrial H+-ATPase

    SciTech Connect

    Huang, Y.; Kantham, L.; Sanadi, D.R.

    1987-03-05

    Repeated extraction of bovine heart submitochondrial particles with ammonia and EDTA (AE) yields a preparation that is highly deficient in coupling factor B (FB). The activity of the thrice extracted particle (AE-P3) in ATP-driven NAD+ reduction by succinate and the /sup 32/Pi-ATP exchange activity were substantially stimulated, 8-fold and 5-fold, respectively, by purified FB. To decrease the basal activity of the particle further, the residual FB in AE-P3 was inactivated by treatment with the -SH reagent, 4-vinylpyridine. The resulting particle was depleted of F1 by treatment with 3.5 M NaBr. This particle was incorporated into asolectin liposomes alone and in the presence of added FB. Passive proton conduction in the FB-deficient proteoliposomes was negligible and restored in the presence of FB. The H+ conductance was inhibited extensively by oligomycin and partially by F1-ATPase. The results show absolute dependence on FB for functioning of the FO proton channel.

  13. Proton-Coupled Electron Transfer in the Reduction of Carbonyls by Samarium Diiodide-Water Complexes.

    PubMed

    Chciuk, Tesia V; Anderson, William R; Flowers, Robert A

    2016-07-20

    Reduction of carbonyls by SmI2 is significantly impacted by the presence of water, but the fundamental step(s) of initial transfer of a formal hydrogen atom from the SmI2-water reagent system to produce an intermediate radical is not fully understood. In this work, we provide evidence consistent with the reduction of carbonyls by SmI2-water proceeding through proton-coupled electron transfer (PCET). Combined rate and computational studies show that a model aldehyde and ketone are likely reduced through an asynchronous PCET, whereas reduction of a representative lactone occurs through a concerted PCET. In the latter case, concerted PCET is likely a consequence of significantly endergonic initial electron transfer. PMID:27367158

  14. Proton-Nucleus Total Cross Sections in Coupled-Channel Approach

    NASA Technical Reports Server (NTRS)

    Tripathi, R. K.; Wilson, John W.; Cucinotta, Francis A.

    2000-01-01

    Recently, nucleon-nucleon (N-N) cross sections in the medium have been extracted directly from experiment. The in-medium N-N cross sections form the basic ingredients of several heavy-ion scattering approaches including the coupled-channel approach developed at the Langley Research Center. In the present study the ratio of the real to the imaginary part of the two-body scattering amplitude in the medium was investigated. These ratios are used in combination with the in-medium N-N cross sections to calculate total proton-nucleus cross sections. The agreement is excellent with the available experimental data. These cross sections are needed for the radiation risk assessment of space missions.

  15. Elastic Proton Scattering of Medium Mass Nuclei from Coupled-Cluster Theory

    SciTech Connect

    Hagen, G.; MichelN.,

    2012-01-01

    Using coupled-cluster theory and interactions from chiral effective field theory, we compute overlap functions for transfer and scattering of low-energy protons on the target nucleus 40Ca. Effects of three-nucleon forces are included phenomenologically as in-medium two-nucleon interactions. Using known asymptotic forms for one-nucleon overlap functions we derive a simple and intuitive way of computing scattering observables such as elastic scattering phase shifts and cross sections. As a first application and proof of principle, we compute phase shifts and differential interaction cross sections at energies of 9.6 and 12.44 MeV and compare with experimental data. Our computed diffraction minima are in fair agreement with experimental results, while we tend to overestimate the cross sections at large scattering angles.

  16. Catalytic Alkene Carboaminations Enabled by Oxidative Proton-Coupled Electron Transfer

    PubMed Central

    Choi, Gilbert J.; Knowles, Robert R.

    2015-01-01

    Here we describe a dual catalyst system comprised of an iridium photocatalyst and weak phosphate base that is capable of both selectively homolyzing the N–H bonds of N-arylamides (bond dissociation free energies ~ 100 kcal/mol) via concerted proton-coupled electron transfer (PCET) and mediating efficient carboamination reactions of the resulting amidyl radicals. This manner of PCET activation, which finds its basis in numerous biological redox processes, enables the formal homolysis of a stronger amide N–H bond in the presence of weaker allylic C–H bonds, a selectivity that is uncommon in conventional molecular H atom acceptors. Moreover, this transformation affords access to a broad range of structurally complex heterocycles from simple amide starting materials. The design, synthetic scope, and mechanistic evaluation of the PCET process are described. PMID:26166022

  17. SOPPA and CCSD vibrational corrections to NMR indirect spin-spin coupling constants of small hydrocarbons

    SciTech Connect

    Faber, Rasmus; Sauer, Stephan P. A.

    2015-12-31

    We present zero-point vibrational corrections to the indirect nuclear spin-spin coupling constants in ethyne, ethene, cyclopropene and allene. The calculations have been carried out both at the level of the second order polarization propagator approximation (SOPPA) employing a new implementation in the DALTON program, at the density functional theory level with the B3LYP functional employing also the Dalton program and at the level of coupled cluster singles and doubles (CCSD) theory employing the implementation in the CFOUR program. Specialized coupling constant basis sets, aug-cc-pVTZ-J, have been employed in the calculations. We find that on average the SOPPA results for both the equilibrium geometry values and the zero-point vibrational corrections are in better agreement with the CCSD results than the corresponding B3LYP results. Furthermore we observed that the vibrational corrections are in the order of 5 Hz for the one-bond carbon-hydrogen couplings and about 1 Hz or smaller for the other couplings apart from the one-bond carbon-carbon coupling (11 Hz) and the two-bond carbon-hydrogen coupling (4 Hz) in ethyne. However, not for all couplings lead the inclusion of zero-point vibrational corrections to better agreement with experiment.

  18. SOPPA and CCSD vibrational corrections to NMR indirect spin-spin coupling constants of small hydrocarbons

    NASA Astrophysics Data System (ADS)

    Faber, Rasmus; Sauer, Stephan P. A.

    2015-12-01

    We present zero-point vibrational corrections to the indirect nuclear spin-spin coupling constants in ethyne, ethene, cyclopropene and allene. The calculations have been carried out both at the level of the second order polarization propagator approximation (SOPPA) employing a new implementation in the DALTON program, at the density functional theory level with the B3LYP functional employing also the Dalton program and at the level of coupled cluster singles and doubles (CCSD) theory employing the implementation in the CFOUR program. Specialized coupling constant basis sets, aug-cc-pVTZ-J, have been employed in the calculations. We find that on average the SOPPA results for both the equilibrium geometry values and the zero-point vibrational corrections are in better agreement with the CCSD results than the corresponding B3LYP results. Furthermore we observed that the vibrational corrections are in the order of 5 Hz for the one-bond carbon-hydrogen couplings and about 1 Hz or smaller for the other couplings apart from the one-bond carbon-carbon coupling (11 Hz) and the two-bond carbon-hydrogen coupling (4 Hz) in ethyne. However, not for all couplings lead the inclusion of zero-point vibrational corrections to better agreement with experiment.

  19. Transport Properties of Ibuprofen Encapsulated in Cyclodextrin Nanosponge Hydrogels: A Proton HR-MAS NMR Spectroscopy Study.

    PubMed

    Ferro, Monica; Castiglione, Franca; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco; Mele, Andrea

    2016-01-01

    The chemical cross-linking of β-cyclodextrin (β-CD) with ethylenediaminetetraacetic dianhydride (EDTA) led to branched polymers referred to as cyclodextrin nanosponges (CDNSEDTA). Two different preparations are described with 1:4 and 1:8 CD-EDTA molar ratios. The corresponding cross-linked polymers were contacted with 0.27 M aqueous solution of ibuprofen sodium salt (IP) leading to homogeneous, colorless, drug loaded hydrogels. The systems were characterized by high resolution magic angle spinning (HR-MAS) NMR spectroscopy. Pulsed field gradient spin echo (PGSE) NMR spectroscopy was used to determine the mean square displacement (MSD) of IP inside the polymeric gel at different observation times td. The data were further processed in order to study the time dependence of MSD: MSD = f(td). The proposed methodology is useful to characterize the different diffusion regimes that, in principle, the solute may experience inside the hydrogel, namely normal or anomalous diffusion. The full protocols including the polymer preparation and purification, the obtainment of drug-loaded hydrogels, the NMR sample preparation, the measurement of MSD by HR-MAS NMR spectroscopy and the final data processing to achieve the time dependence of MSD are here reported and discussed. The presented experiments represent a paradigmatic case and the data are discussed in terms of innovative approach to the characterization of the transport properties of an encapsulated guest within a polymeric host of potential application for drug delivery. PMID:27585291

  20. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  1. Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings

    PubMed Central

    Bailor, Maximillian H; Musselman, Catherine; Hansen, Alexandar L; Gulati, Kush; Patel, Dinshaw J; Al-Hashimi, Hashim M

    2015-01-01

    We present a protocol for determining the relative orientation and dynamics of A-form helices in 13C/15N isotopically enriched RNA samples using NMR residual dipolar couplings (RDCs). Non-terminal Watson–Crick base pairs in helical stems are experimentally identified using NOE and trans-hydrogen bond connectivity and modeled using the idealized A-form helix geometry. RDCs measured in the partially aligned RNA are used to compute order tensors describing average alignment of each helix relative to the applied magnetic field. The order tensors are translated into Euler angles defining the average relative orientation of helices and order parameters describing the amplitude and asymmetry of interhelix motions. The protocol does not require complete resonance assignments and therefore can be implemented rapidly to RNAs much larger than those for which complete high-resolution NMR structure determination is feasible. The protocol is particularly valuable for exploring adaptive changes in RNA conformation that occur in response to biologically relevant signals. Following resonance assignments, the procedure is expected to take no more than 2 weeks of acquisition and data analysis time. PMID:17571061

  2. Metabolic Profiling and Classification of Propolis Samples from Southern Brazil: An NMR-Based Platform Coupled with Machine Learning.

    PubMed

    Maraschin, Marcelo; Somensi-Zeggio, Amélia; Oliveira, Simone K; Kuhnen, Shirley; Tomazzoli, Maíra M; Raguzzoni, Josiane C; Zeri, Ana C M; Carreira, Rafael; Correia, Sara; Costa, Christopher; Rocha, Miguel

    2016-01-22

    The chemical composition of propolis is affected by environmental factors and harvest season, making it difficult to standardize its extracts for medicinal usage. By detecting a typical chemical profile associated with propolis from a specific production region or season, certain types of propolis may be used to obtain a specific pharmacological activity. In this study, propolis from three agroecological regions (plain, plateau, and highlands) from southern Brazil, collected over the four seasons of 2010, were investigated through a novel NMR-based metabolomics data analysis workflow. Chemometrics and machine learning algorithms (PLS-DA and RF), including methods to estimate variable importance in classification, were used in this study. The machine learning and feature selection methods permitted construction of models for propolis sample classification with high accuracy (>75%, reaching ∼90% in the best case), better discriminating samples regarding their collection seasons comparatively to the harvest regions. PLS-DA and RF allowed the identification of biomarkers for sample discrimination, expanding the set of discriminating features and adding relevant information for the identification of the class-determining metabolites. The NMR-based metabolomics analytical platform, coupled to bioinformatic tools, allowed characterization and classification of Brazilian propolis samples regarding the metabolite signature of important compounds, i.e., chemical fingerprint, harvest seasons, and production regions. PMID:26693586

  3. Coupled Electron and Proton Transfer Reactions during the O→E Transition in Bovine Cytochrome c Oxidase

    PubMed Central

    Popović, Dragan M.; Stuchebrukhov, Alexei A.

    2014-01-01

    A combined DFT/electrostatic approach is employed to study the coupling of proton and electron transfer reactions in cytochrome c oxidase (CcO) and its proton pumping mechanism. The coupling of the chemical proton to the internal electron transfer between heme a and the binuclear center is examined for the O→E transition. The novel features of the His291 pumping model are proposed, which involve timely well-synchronized sequence of the proton-coupled electron transfer reactions. The obtained pKas and Ems of the key ionizable and redox-active groups at the different stages of the O→E transition are consistent with available experimental data. The PT step from E242 to H291 is examined in detail for various redox states of the hemes and various conformations of E242 side-chain. Redox potential calculations of the successive steps in the reaction cycle during the O→E transition are able to explain a cascade of equilibria between the different intermediate states and electron redistribution between the metal centers during the course of the catalytic activity. All four electrometric phases are discussed in the light of the obtained results, providing a robust support for the His291 model of proton pumping in CcO. PMID:22086149

  4. Two-dimensional B- B NMR spectroscopy: coupling through bridging hydrogen atoms

    SciTech Connect

    Gaines, D.F.; Edvenson, G.M.; Hill, T.G.; Adams, B.R.

    1987-06-03

    Application of B- B two-dimensional correlated spectroscopy (COSY) to a variety of boranes and substituted boranes has shown coupling between B nuclei linked by bridging hydrogen atoms to be more common than previously observed. Coupling between the hydrogen-bridged boron nuclei in decaborane(14), 2-(CH3)B5H8, B4H10, (Me2N)2B4H8, ( -Me2NCH2)B5H8, and ( -Me3CCH=N)B5H8 are reported. The factors that contribute to the detection of coupling between hydrogen-bridged boron atoms are discussed.

  5. Comprehensive triblock copolymer analysis by coupled thermal field-flow fractionation-NMR.

    PubMed

    van Aswegen, Werner; Hiller, Wolf; Hehn, Mathias; Pasch, Harald

    2013-07-12

    Thermal field-flow fractionation (ThFFF) is used as a novel fractionation technique to investigate the molecular heterogeneity of PB-b-PVP-b-PtBMA triblock copolymers. Such copolymers cause major problems in liquid chromatography due to very strong polar interactions with the stationary phase. ThFFF separates the copolymers with regard to size and/or chemical composition based on the normal and thermal diffusion coefficients. The separation mechanism in ThFFF and the chemical composition of the separated species is elucidated by online (1) H NMR. Based on the compositional analysis and a calibration of the system with the respective homopolymers, the samples are quantified regarding their molar masses, chemical compositions, and microstructures providing comprehensive information on the complex structure of these block copolymers. PMID:23722993

  6. NMR spin-spin coupling constants: bond angle dependence of the sign and magnitude of the vicinal (3)JHF coupling.

    PubMed

    Viesser, Renan V; Ducati, Lucas C; Autschbach, Jochen; Tormena, Cláudio F

    2016-08-24

    The dependence of the magnitude and sign of (3)JHFF on the bond angle in fluoro-cycloalkene compounds is evaluated by electronic structure calculations using different levels of theory, viz. DFT, SOPPA(CCSD) and SOPPA(CC2). Localized molecular orbital contributions to (3)JHFF are analyzed to assess which orbitals are responsible for (3)JHFF and which are the most important coupling transmission mechanisms for each compound. Fluoro-ethylene is used as a model system to evaluate the dependence of the (3)JHFF coupling constant on the angle between the σCα-F and σCα'-HF vectors. Through-space and hyperconjugative transmission pathways and ring strain are identified as responsible for the opposite trend between (3)JHFF and bond angle, and for the negative signs obtained for the two molecules, respectively. One of the fluorine lone pairs, σCα'-HF, σCα-F, σCα'-Cβ' bonding orbitals and the σ*Cα-F antibonding orbital are involved in the J-coupling pathways, according to analyses of pairwise-steric and hyperconjugative energies. PMID:27526856

  7. Metal-free aqueous redox capacitor via proton rocking-chair system in an organic-based couple.

    PubMed

    Tomai, Takaaki; Mitani, Satoshi; Komatsu, Daiki; Kawaguchi, Yuji; Honma, Itaru

    2014-01-01

    Safe and inexpensive energy storage devices with long cycle lifetimes and high power and energy densities are mandatory for the development of electrical power grids that connect with renewable energy sources. In this study, we demonstrated metal-free aqueous redox capacitors using couples comprising low-molecular-weight organic compounds. In addition to the electric double layer formation, proton insertion/extraction reactions between a couple consisting of inexpensive quinones/hydroquinones contributed to the energy storage. This energy storage mechanism, in which protons are shuttled back and forth between two electrodes upon charge and discharge, can be regarded as a proton rocking-chair system. The fabricated capacitor showed a large capacity (>20 Wh/kg), even in the applied potential range between 0-1 V, and high power capability (>5 A/g). The support of the organic compounds in nanoporous carbon facilitated the efficient use of the organic compounds with a lifetime of thousands of cycles. PMID:24395117

  8. Multidimensional treatment of stochastic solvent dynamics in photoinduced proton-coupled electron transfer processes: sequential, concerted, and complex branching mechanisms.

    PubMed

    Soudackov, Alexander V; Hazra, Anirban; Hammes-Schiffer, Sharon

    2011-10-14

    A theoretical approach for the multidimensional treatment of photoinduced proton-coupled electron transfer (PCET) processes in solution is presented. This methodology is based on the multistate continuum theory with an arbitrary number of diabatic electronic states representing the relevant charge distributions in a general PCET system. The active electrons and transferring proton(s) are treated quantum mechanically, and the electron-proton vibronic free energy surfaces are represented as functions of multiple scalar solvent coordinates corresponding to the single electron and proton transfer reactions involved in the PCET process. A dynamical formulation of the dielectric continuum theory is used to derive a set of coupled generalized Langevin equations of motion describing the time evolution of these collective solvent coordinates. The parameters in the Langevin equations depend on the solvent properties, such as the dielectric constants, relaxation time, and molecular moment of inertia, as well as the solute properties. The dynamics of selected intramolecular nuclear coordinates, such as the proton donor-acceptor distance or a torsional angle within the PCET complex, may also be included in this formulation. A surface hopping method in conjunction with the Langevin equations of motion is used to simulate the nonadiabatic dynamics on the multidimensional electron-proton vibronic free energy surfaces following photoexcitation. This theoretical treatment enables the description of both sequential and concerted mechanisms, as well as more complex processes involving a combination of these mechanisms. The application of this methodology to a series of model systems corresponding to collinear and orthogonal PCET illustrates fundamental aspects of these different mechanisms and elucidates the significance of proton vibrational relaxation and nonequilibrium solvent dynamics. PMID:22010706

  9. Regulating proton-coupled electron transfer for efficient water splitting by manganese oxides at neutral pH

    PubMed Central

    Yamaguchi, Akira; Inuzuka, Riko; Takashima, Toshihiro; Hayashi, Toru; Hashimoto, Kazuhito; Nakamura, Ryuhei

    2014-01-01

    Manganese oxides have been extensively investigated as model systems for the oxygen-evolving complex of photosystem II. However, most bioinspired catalysts are inefficient at neutral pH and functional similarity to the oxygen-evolving complex has been rarely achieved with manganese. Here we report the regulation of proton-coupled electron transfer involved in water oxidation by manganese oxides. Pyridine and its derivatives, which have pKa values intermediate to the water ligand bound to manganese(II) and manganese(III), are used as proton-coupled electron transfer induction reagents. The induction of concerted proton-coupled electron transfer is demonstrated by the detection of deuterium kinetic isotope effects and compliance of the reactions with the libido rule. Although proton-coupled electron transfer regulation is essential for the facial redox change of manganese in photosystem II, most manganese oxides impair these regulatory mechanisms. Thus, the present findings may provide a new design rationale for functional analogues of the oxygen-evolving complex for efficient water splitting at neutral pH. PMID:24977746

  10. Virtual coupling potential for elastic scattering of 10,11Be on proton and carbon targets

    NASA Astrophysics Data System (ADS)

    Lapoux, V.; Alamanos, N.; Auger, F.; Blumenfeld, Y.; Casandjian, J.-M.; Chartier, M.; Cortina-Gil, M. D.; Fékou-Youmbi, V.; Gillibert, A.; Cormick, M. Mac; Maréchal, F.; Marie, F.; Mittig, W.; de Oliveira Santos, F.; Orr, N. A.; Ostrowski, A. N.; Ottini-Hustache, S.; Roussel-Chomaz, P.; Scarpaci, J.-A.; Sida, J.-L.; Suomijärvi, T.; Winfield, J. S.

    2008-01-01

    The 10,11Be(p, p) and (12C, 12C) reactions were analyzed to determine the influence of the weak binding energies of exotic nuclei on their interaction potential. The elastic cross sections were measured at GANIL in inverse kinematics using radioactive 10,11Be beams produced at energies of 39.1A and 38.4 A MeV. The elastic proton scattering data were analyzed within the framework of the microscopic Jeukenne-Lejeune-Mahaux (JLM) nucleon-nucleus potential. The angular distributions are found to be best reproduced by reducing the real part of the microscopic optical potential, as a consequence of the coupling to the continuum. These effects modify deeply the elastic potential. Including the Virtual Coupling Potential (VCP), we show the ability of the general optical potentials to reproduce the data for scattering of unstable nuclei, using realistic densities. Finally, the concepts needed to develop a more general and microscopic approach of the VCP are discussed.

  11. Photochemical Tyrosine Oxidation in the Structurally Well-Defined α3Y Protein: Proton-Coupled Electron Transfer and a Long-Lived Tyrosine Radical

    PubMed Central

    2014-01-01

    Tyrosine oxidation–reduction involves proton-coupled electron transfer (PCET) and a reactive radical state. These properties are effectively controlled in enzymes that use tyrosine as a high-potential, one-electron redox cofactor. The α3Y model protein contains Y32, which can be reversibly oxidized and reduced in voltammetry measurements. Structural and kinetic properties of α3Y are presented. A solution NMR structural analysis reveals that Y32 is the most deeply buried residue in α3Y. Time-resolved spectroscopy using a soluble flash-quench generated [Ru(2,2′-bipyridine)3]3+ oxidant provides high-quality Y32–O• absorption spectra. The rate constant of Y32 oxidation (kPCET) is pH dependent: 1.4 × 104 M–1 s–1 (pH 5.5), 1.8 × 105 M–1 s–1 (pH 8.5), 5.4 × 103 M–1 s–1 (pD 5.5), and 4.0 × 104 M–1 s–1 (pD 8.5). kH/kD of Y32 oxidation is 2.5 ± 0.5 and 4.5 ± 0.9 at pH(D) 5.5 and 8.5, respectively. These pH and isotope characteristics suggest a concerted or stepwise, proton-first Y32 oxidation mechanism. The photochemical yield of Y32–O• is 28–58% versus the concentration of [Ru(2,2′-bipyridine)3]3+. Y32–O• decays slowly, t1/2 in the range of 2–10 s, at both pH 5.5 and 8.5, via radical–radical dimerization as shown by second-order kinetics and fluorescence data. The high stability of Y32–O• is discussed relative to the structural properties of the Y32 site. Finally, the static α3Y NMR structure cannot explain (i) how the phenolic proton released upon oxidation is removed or (ii) how two Y32–O• come together to form dityrosine. These observations suggest that the dynamic properties of the protein ensemble may play an essential role in controlling the PCET and radical decay characteristics of α3Y. PMID:25121576

  12. Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

    PubMed Central

    Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John-Paul; Schrader, Tobias E.; Ostermann, Andreas; Kovalevsky, Andrey Y.; McKenna, Robert; Fisher, Suzanne Zoë

    2015-01-01

    Human carbonic anhydrase II (HCA II) uses a Zn-bound OH−/H2O mechanism to catalyze the reversible hydration of CO2. This catalysis also involves a separate proton transfer step, mediated by an ordered solvent network coordinated by hydrophilic residues. One of these residues, Tyr7, was previously shown to be deprotonated in the neutron crystal structure at pH 10. This observation indicated that Tyr7 has a perturbed pKa compared with free tyrosine. To further probe the pKa of this residue, NMR spectroscopic measurements of [13C]Tyr-labeled holo HCA II (with active-site Zn present) were preformed to titrate all Tyr residues between pH 5.4–11.0. In addition, neutron studies of apo HCA II (with Zn removed from the active site) at pH 7.5 and holo HCA II at pH 6 were conducted. This detailed interrogation of tyrosines in HCA II by NMR and neutron crystallography revealed a significantly lowered pKa of Tyr7 and how pH and Tyr proximity to Zn affect hydrogen-bonding interactions. PMID:25902526

  13. Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer.

    PubMed

    Michalczyk, Ryszard; Unkefer, Clifford J; Bacik, John-Paul; Schrader, Tobias E; Ostermann, Andreas; Kovalevsky, Andrey Y; McKenna, Robert; Fisher, Suzanne Zoë

    2015-05-01

    Human carbonic anhydrase II (HCA II) uses a Zn-bound OH(-)/H2O mechanism to catalyze the reversible hydration of CO2. This catalysis also involves a separate proton transfer step, mediated by an ordered solvent network coordinated by hydrophilic residues. One of these residues, Tyr7, was previously shown to be deprotonated in the neutron crystal structure at pH 10. This observation indicated that Tyr7 has a perturbed pKa compared with free tyrosine. To further probe the pKa of this residue, NMR spectroscopic measurements of [(13)C]Tyr-labeled holo HCA II (with active-site Zn present) were preformed to titrate all Tyr residues between pH 5.4-11.0. In addition, neutron studies of apo HCA II (with Zn removed from the active site) at pH 7.5 and holo HCA II at pH 6 were conducted. This detailed interrogation of tyrosines in HCA II by NMR and neutron crystallography revealed a significantly lowered pKa of Tyr7 and how pH and Tyr proximity to Zn affect hydrogen-bonding interactions. PMID:25902526

  14. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition.

    PubMed

    Harika, Narinder K; Paul, Ananya; Stroeva, Ekaterina; Chai, Yun; Boykin, David W; Germann, Markus W; Wilson, W David

    2016-06-01

    Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor-surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a (15)N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents. PMID:27131382

  15. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition

    PubMed Central

    Harika, Narinder K.; Paul, Ananya; Stroeva, Ekaterina; Chai, Yun; Boykin, David W.; Germann, Markus W.; Wilson, W. David

    2016-01-01

    Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents. PMID:27131382

  16. Measurement of Heteronuclear Dipolar Coupling by Transferred-Echo Double-Resonance NMR

    NASA Astrophysics Data System (ADS)

    Hing, A. W.; Vega, S.; Schaefer, J.

    A magic-angle spinning experiment called transferred-echo double resonance (TEDOR) has been introduced recently to measure the I-S dipolar coupling of heteronuclear I-S pairs of spin- {1}/{2} nuclei while eliminating unwanted background signals from uncoupled I and S spins via a coherence-transfer process. In this paper, a quantitative description of the TEDOR experiment is given in terms of the evolution of the density matrix for a pair of heteronuclear spins. The resulting equations provide a theoretical basis for evaluating the selectivity and sensitivity of TEDOR and suggest strategies for determining dipolar coupling constants directly from TEDOR data. Experimental examples illustrating these aspects of TEDOR are provided by studies performed on a range of 13C- 15N dipolar couplings found in double-labeled asparagine, alanine, glycine, and the linear peptide antibiotic, gramicidin.

  17. ⁵¹V NMR Crystallography of Vanadium Chloroperoxidase and Its Directed Evolution P395D/L241V/T343A Mutant: Protonation Environments of the Active Site.

    PubMed

    Gupta, Rupal; Hou, Guangjin; Renirie, Rokus; Wever, Ron; Polenova, Tatyana

    2015-04-29

    Vanadium-dependent haloperoxidases (VHPOs) perform two-electron oxidation of halides using hydrogen peroxide. Their mechanism, including the factors determining the substrate specificity and the pH-dependence of the catalytic rates, is poorly understood. The vanadate cofactor in the active site of VHPOs contains "spectroscopically silent" V(V), which does not change oxidation state during the reaction. We employed an NMR crystallography approach based on (51)V magic angle spinning NMR spectroscopy and Density Functional Theory, to gain insights into the structure and coordination environment of the cofactor in the resting state of vanadium-dependent chloroperoxidases (VCPO). The cofactor environments in the wild-type VCPO and its P395D/L241V/T343A mutant exhibiting 5-100-fold improved catalytic activity are examined at various pH values. Optimal sensitivity attained due to the fast MAS probe technologies enabled the assignment of the location and number of protons on the vanadate as a function of pH. The vanadate cofactor changes its protonation from quadruply protonated at pH 6.3 to triply protonated at pH 7.3 to doubly protonated at pH 8.3. In contrast, in the mutant, the vanadate protonation is the same at pH 5.0 and 8.3, and the cofactor is doubly protonated. This methodology to identify the distinct protonation environments of the cofactor, which are also pH-dependent, could help explain the different reactivities of the wild-type and mutant VCPO and their pH-dependence. This study demonstrates that (51)V-based NMR crystallography can be used to derive the detailed coordination environments of vanadium centers in large biological molecules. PMID:25856001

  18. Proton-coupled electron transfer at modified electrodes by multiple pathways

    SciTech Connect

    Chen, Z.; Vannucci, A. K.; Concepcion, J. J.; Jurss, J. W.; Meyer, T. J.

    2011-12-12

    In single site water or hydrocarbon oxidation catalysis with polypyridyl Ru complexes such as [RuII(Mebimpy)(bpy)(H₂O)]2+ [where bpy is 2,2'-bipyridine, and Mebimpy is 2,6-bis(1-methylbenzimidazol-2-yl)pyridine] 2, or its surface-bound analog [RuII(Mebimpy)(4,4'-bis-methlylenephosphonato-2,2'-bipyridine)(OH₂)]2+ 2-PO₃H₂, accessing the reactive states, RuV = O3+/RuIV = O2+, at the electrode interface is typically rate limiting. The higher oxidation states are accessible by proton-coupled electron transfer oxidation of aqua precursors, but access at inert electrodes is kinetically inhibited. The inhibition arises from stepwise mechanisms which impose high energy barriers for 1e- intermediates. Oxidation of the RuIII-OH2+ or RuIII-OH₂3+ forms of 2-PO₃H₂ to RuIV = O2+ on planar fluoride-doped SnO₂ electrode and in nanostructured films of Sn(IV)-doped In₂O₃ and TiO₂ has been investigated with a focus on identifying microscopic phenomena. The results provide direct evidence for important roles for the nature of the electrode, temperature, surface coverage, added buffer base, pH, solvent, and solvent H₂O/D₂O isotope effects. In the nonaqueous solvent, propylene carbonate, there is evidence for a role for surface-bound phosphonate groups as proton acceptors.

  19. Thermodynamic investigation into the mechanisms of proton-coupled electron transfer events in heme protein maquettes.

    PubMed

    Reddi, Amit R; Reedy, Charles J; Mui, Steven; Gibney, Brian R

    2007-01-01

    To study the engineering requirements for proton pumping in energy-converting enzymes such as cytochrome c oxidase, the thermodynamics and mechanisms of proton-coupled electron transfer in two designed heme proteins are elucidated. Both heme protein maquettes chosen, heme b-[H10A24]2 and heme b-[delta7-His]2, are four-alpha-helix bundles that display pH-dependent heme midpoint potential modulations, or redox-Bohr effects. Detailed equilibrium binding studies of ferric and ferrous heme b with these maquettes allow the individual contributions of heme-protein association, iron-histidine ligation, and heme-protein electrostatics to be elucidated. These data demonstrate that the larger, less well-structured [H10A24]2 binds heme b in both oxidation states tighter than the smaller and more well-structured [Delta7-His]2 due to a stronger porphyrin-protein hydrophobic interaction. The 66 mV (1.5 kcal/mol) difference in their heme reduction potentials observed at pH 8.0 is due mostly to stabilization of ferrous heme in [H10A24]2 relative to [delta7-His]2. The data indicate that porphyrin-protein hydrophobic interactions and heme iron coordination are responsible for the Kd value of 37 nM for the heme b-[delta7-His]2 scaffold, while the affinity of heme b for [H10A24]2 is 20-fold tighter due to a combination of porphyrin-protein hydrophobic interactions, iron coordination, and electrostatic effects. The data also illustrate that the contribution of bis-His coordination to ferrous heme protein affinity is limited, <3.0 kcal/mol. The 1H+/1e- redox-Bohr effect of heme b-[H10A24]2 is due to the greater absolute stabilization of the ferric heme (4.1 kcal/mol) compared to the ferrous heme (1.4 kcal/mol) binding upon glutamic acid deprotonation, i.e., an electrostatic response mechanism. The 2H+/1e- redox-Bohr effect observed for heme b-[delta7-His]2 is due to histidine protonation and histidine dissociation of ferrous heme b upon reduction, i.e., a ligand loss mechanism. These

  20. Membrane Protein Structure and Dynamics from NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hong, Mei; Zhang, Yuan; Hu, Fanghao

    2012-05-01

    We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca2+ pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.

  1. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    NASA Astrophysics Data System (ADS)

    Mori, Yukie; Masuda, Yuichi

    2015-09-01

    Hydrogen phthalate anion has a short strong O-H-O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl4, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17O and 1H nuclei monitoring the nuclear magnetic relaxation times of 1H. The experimental results indicated that the H-bond geometry of 2 is influenced by the interactions with dimethylsulfoxide, suggesting the formation of a bifurcated H-bond, which was supported by the DFT calculations. The MD simulations for the methanol solution of 2 showed that the asymmetry of the OH distance is correlated with the asymmetry in the electrostatic field of the

  2. Drug-induced conformational and dynamical changes of the S31N mutant of the influenza M2 proton channel investigated by solid-state NMR.

    PubMed

    Williams, Jonathan K; Tietze, Daniel; Wang, Jun; Wu, Yibing; DeGrado, William F; Hong, Mei

    2013-07-01

    The M2 protein of influenza A viruses forms a tetrameric proton channel that is targeted by the amantadine class of antiviral drugs. A S31N mutation in the transmembrane (TM) domain of the protein has caused widespread amantadine resistance in most of the currently circulating flu viruses. Recently, a new family of compounds based on amantadine- and aryl-substituted isoxazole were discovered to inhibit the S31N channel activity and reduce replication of S31N-harboring viruses. We now use solid-state NMR spectroscopy to investigate the effects of one of these isoxazole compounds, WJ352, on the conformation of the S31N TM segment and the dynamics of the proton-selective residue, His37. Chemical shift perturbations show that WJ352 changes the conformational equilibrium of multiple TM residues, with the maximal perturbation occurring at the crucial Asn31. (13)C-(2)H distance measurements and (1)H-(1)H NOE cross peaks indicate that the adamantane moiety of the drug is bound in the spacious pore between Asn31 and Gly34 while the phenyl tail is located near Val27. Thus, the polar amine points to the channel exterior rather than to His37, in contrast to amantadine and rimantadine in the wild-type channel, suggesting that the drug is significantly stabilized by hydrophobic interactions between the adamantane and the TM peptide. (15)N and (13)C chemical shifts indicate that at low pH, His37 undergoes fast exchange among the τ tautomer, the π tautomer, and the cationic state due to proton transfer with water. The exchange rate is higher than the wild-type channel, consistent with the larger single-channel conductance of the mutant. Drug binding at acidic pH largely suppresses this exchange, reverting the histidines to a similar charge distribution as that of the high-pH closed state. PMID:23758317

  3. Tyrosine analogues for probing proton-coupled electron transfer processes in peptides and proteins.

    PubMed

    Nara, Susheel J; Valgimigli, Luca; Pedulli, Gian Franco; Pratt, Derek A

    2010-01-20

    A series of amino acids analogous to tyrosine, but differing in the physicochemical properties of the aryl alcohol side chain, have been prepared and characterized. These compounds are expected to be useful in understanding the relationships between structure, thermodynamics, and kinetics in long-range proton-coupled electron transfer processes in peptides and proteins. Systematic changes in the acidity, redox potential, and O-H bond strength of the tyrosine side chain could be induced upon substituting the phenol for pyridinol and pyrimidinol moieties. Further modulation was possible by introducing methyl and t-butyl substitution in the position ortho to the phenolic hydroxyl. The unnatural amino acids were prepared by Pd-catalyzed cross-coupling of the corresponding halogenated aryl alcohol protected as their benzyl ethers with an organozinc reagent derived from N-Boc L-serine carboxymethyl ester. Subsequent debenzylation by catalytic hydrogenation yielded the tyrosine analogues in good yield. Spectrophotometric titrations revealed a decrease in tyrosine pK(a) of ca. 1.5 log units per included nitrogen atom, along with a corresponding increase in the oxidation (peak) potentials of ca. 200 mV, respectively. All told, the six novel amino acids described here have phenol-like side chains with pK(a)'s that span a range of 7.0 to greater than 10, and an oxidation (peak) potential range of greater than 600 mV at and around physiological pH. Radical equilibration EPR experiments were carried out to reveal that the O-H bond strengths increase systematically upon nitrogen incorporation (by ca. 0.5-1.0 kcal/mol), and radical stability and persistence increase systematically upon introduction of alkyl substitution in the ortho positions. The EPR spectra of the aryloxyl radicals derived from tyrosine and each of the analogues could be determined at room temperature, and each featured distinct spectral properties. The uniqueness of their spectra will be helpful in discerning

  4. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil.

    PubMed

    Litvak, Ilya M; Espinosa, Catalina A; Shapiro, Rebecca A; Oldham, Andrew N; Duong, Vincent V; Martin, Rachel W

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds. PMID:20673643

  5. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil

    NASA Astrophysics Data System (ADS)

    Litvak, Ilya M.; Espinosa, Catalina A.; Shapiro, Rebecca A.; Oldham, Andrew N.; Duong, Vincent V.; Martin, Rachel W.

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds.

  6. Solid-state Hadamard NMR spectroscopy: Simultaneous measurements of multiple selective homonuclear scalar couplings

    NASA Astrophysics Data System (ADS)

    Kakita, Veera Mohana Rao; Kupče, Eriks; Bharatam, Jagadeesh

    2015-02-01

    Unambiguous measurement of homonuclear scalar couplings (J) in multi-spin scalar network systems is not straightforward. Further, the direct measurement of J-couplings is obscured in solid-state samples due to the dipolar and chemical shift anisotropy (CSA)-dominated line broadening, even under the magic angle spinning (MAS). We present a new multiple frequency selective spin-echo method based on Hadamard matrix encoding, for simultaneous measurement of multiple homonuclear scalar couplings (J) in the solid-state. In contrast to the Hadamard encoded selective excitation schemes known for the solution-state, herein the selectivity is achieved during refocusing period. The Hadamard encoded refocusing scheme concurrently allows to create the spin-spin commutation property between number of spin-pairs of choice in uniformly labelled molecules, which, therefore avoids (1) the repetition of the double selective refocusing experiments for each spin-pair and (2) the synthesis of expensive selective labelled molecules. The experimental scheme is exemplified for determining 1JCC and 3JCC values in 13C6L-Histidine.HCl molecule, which are found to be in excellent agreement with those measured in conventional double frequency selective refocusing mode as well as in the solution-state. This method can be simply extended to 2D/3D pulse schemes and be applied to small bio-molecular solids.

  7. Solid-state Hadamard NMR spectroscopy: simultaneous measurements of multiple selective homonuclear scalar couplings.

    PubMed

    Kakita, Veera Mohana Rao; Kupče, Eriks; Bharatam, Jagadeesh

    2015-02-01

    Unambiguous measurement of homonuclear scalar couplings (J) in multi-spin scalar network systems is not straightforward. Further, the direct measurement of J-couplings is obscured in solid-state samples due to the dipolar and chemical shift anisotropy (CSA)-dominated line broadening, even under the magic angle spinning (MAS). We present a new multiple frequency selective spin-echo method based on Hadamard matrix encoding, for simultaneous measurement of multiple homonuclear scalar couplings (J) in the solid-state. In contrast to the Hadamard encoded selective excitation schemes known for the solution-state, herein the selectivity is achieved during refocusing period. The Hadamard encoded refocusing scheme concurrently allows to create the spin-spin commutation property between number of spin-pairs of choice in uniformly labelled molecules, which, therefore avoids (1) the repetition of the double selective refocusing experiments for each spin-pair and (2) the synthesis of expensive selective labelled molecules. The experimental scheme is exemplified for determining (1)JCC and (3)JCC values in (13)C6l-Histidine.HCl molecule, which are found to be in excellent agreement with those measured in conventional double frequency selective refocusing mode as well as in the solution-state. This method can be simply extended to 2D/3D pulse schemes and be applied to small bio-molecular solids. PMID:25554944

  8. Probing the coupling between proton and electron transfer in Photosystem II core complexes containing a 3-fluorotyrosine

    PubMed Central

    Rappaport, Fabrice; Boussac, Alain; Force, Dee Ann; Peloquin, Jeffrey; Brynda, Marcin; Sugiura, Miwa; Un, Sun; Britt, R. David; Diner, Bruce A.

    2009-01-01

    The catalytic cycle of numerous enzymes involves the coupling between proton transfer and electron transfer. Yet, the understanding of this coordinated transfer in biological systems remains limited, likely because its characterization relies on the controlled but experimentally challenging modifications of the free energy changes associated with either the electron or proton transfer. We have performed such a study here in Photosystem II. The driving force for electron transfer from TyrZ to P680•+ has been decreased by ~ 80 meV by mutating the axial ligand of P680, and that for proton transfer upon oxidation of TyrZ by substituting a 3-fluorotyrosine (3F-TyrZ) for TyrZ. In Mn-depleted Photosystem II, the dependence upon pH of the oxidation rates of TyrZ and 3F-TyrZ were found to be similar. However, in the pH range where the phenolic hydroxyl of TyrZ is involved in a H-bond with a proton acceptor, the activation energy of the oxidation of 3F-TyrZ is decreased by 110 meV, a value which correlates with the in vitro finding of a 90 meV stabilization energy to the phenolate form of 3F-Tyr when compared to Tyr (Seyedsayamdost et al., 2006, JACS 128:1569–79). Thus, when the phenol of YZ acts as a H-bond-donor, its oxidation by P680•+ is controlled by its prior deprotonation. This contrasts with the situation prevailing at lower pH, where the proton acceptor is protonated and therefore unavailable, in which the oxidation-induced proton transfer from the phenolic hydroxyl of TyrZ has been proposed to occur concertedly with the electron transfer to P680•+. This suggests a switch between a concerted proton/electron transfer at pHs < 7.5 to a sequential one at pHs > 7.5 and illustrates the roles of the H-bond and of the likely salt-bridge existing between the phenolate and the nearby proton acceptor in determining the coupling between proton and electron transfer. PMID:19265377

  9. Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations.

    PubMed

    Oliveira, A Sofia F; Campos, Sara R R; Baptista, António M; Soares, Cláudio M

    2016-06-01

    Cytochrome c oxidases (CcOs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes reduce dioxygen (O2) to water and, simultaneously, generate a transmembrane electrochemical proton gradient. Despite their importance in the aerobic metabolism and the large amount of structural and biochemical data available for the A1-type CcO family, there is still no consensually accepted description of the molecular mechanisms operating in this protein. A substantial number of questions about the CcO's working mechanism remain to be answered, including how the protonation behavior of some key residues is modulated during a reduction cycle and how is the conformation of the protein affected by protonation. The main objective of this work was to study the protonation-conformation coupling in CcOs and identify the molecular factors that control the protonation state of some key residues. In order to directly capture the interplay between protonation and conformational effects, we have performed constant-pH MD simulations of an A1-type CcO inserted into a lipid bilayer in two redox states (oxidized and reduced) at physiological pH. From the simulations, we were able to identify several groups with unusual titration behavior that are highly dependent on the protein redox state, including the A-propionate from heme a and the D-propionate from heme a3, two key groups possibly involved in proton pumping. The protonation state of these two groups is heavily influenced by subtle conformational changes in the protein (notably of R481I and R482I) and by small changes in the hydrogen bond network. PMID:27033303

  10. Inelastic dark matter with spin-dependent couplings to protons and large modulation fractions in DAMA

    NASA Astrophysics Data System (ADS)

    Scopel, Stefano; Yoon, Kook-Hyun

    2016-02-01

    We discuss a scenario where the DAMA modulation effect is explained by a Weakly Interacting Massive Particle (WIMP) which upscatters inelastically to a heavier state and predominantly couples to the spin of protons. In this scenario constraints from xenon and germanium targets are evaded dynamically, due to the suppression of the WIMP coupling to neutrons, while those from fluorine targets are evaded kinematically, because the minimal WIMP incoming speed required to trigger upscatters off fluorine exceeds the maximal WIMP velocity in the Galaxy, or is very close to it. In this scenario WIMP scatterings off sodium are usually sensitive to the large-speed tail of the WIMP velocity distribution and modulated fractions of the signal close to unity arise in a natural way. On the other hand, a halo-independent analysis with more conservative assumptions about the WIMP velocity distribution allows to extend the viable parameter space to configurations where large modulated fractions are not strictly necessary. We discuss large modulated fractions in the Maxwellian case showing that they imply a departure from the usual cosine time dependence of the expected signal in DAMA. However we explicitly show that the DAMA data is not sensitive to this distortion, both in time and frequency space, even in the extreme case of a 100 % modulated fraction. Moreover the same scenario provides an explanation of the maximum in the energy spectrum of the modulation amplitude detected by DAMA in terms of WIMPs whose minimal incoming speed matches the kinematic threshold for inelastic upscatters. For the elastic case the detection of such maximum suggests an inversion of the modulation phase below the present DAMA energy threshold, while this is not expected for inelastic scattering. This may allow to discriminate between the two scenarios in a future low-threshold analysis of the DAMA data.

  11. Functional elements in the minimal promoter of the human proton-coupled folate transporter

    SciTech Connect

    Stark, Michal; Gonen, Nitzan; Assaraf, Yehuda G.

    2009-10-09

    The proton-coupled folate transporter (PCFT) is the dominant intestinal folate transporter, however, its promoter has yet to be revealed. Hence, we here cloned a 3.1 kb fragment upstream to the first ATG of the human PCFT gene and generated sequential deletion constructs evaluated in luciferase reporter assay. This analysis mapped the minimal promoter to 157 bp upstream to the first ATG. Crucial GC-box sites were identified within the minimal promoter and in its close vicinity which substantially contribute to promoter activity, as their disruption resulted in 94% loss of luciferase activity. We also identified upstream enhancer elements including YY1 and AP1 which, although distantly located, prominently transactivated the minimal promoter, as their inactivation resulted in 50% decrease in reporter activity. This is the first functional identification of the minimal PCFT promoter harboring crucial GC-box elements that markedly contribute to its transcriptional activation via putative interaction with distal YY1 and AP1 enhancer elements.

  12. Tyrosine oxidation in heme oxygenase: examination of long-range proton-coupled electron transfer.

    PubMed

    Smirnov, Valeriy V; Roth, Justine P

    2014-10-01

    Heme oxygenase is responsible for the degradation of a histidine-ligated ferric protoporphyrin IX (Por) to biliverdin, CO, and the free ferrous ion. Described here are studies of tyrosyl radical formation reactions that occur after oxidizing Fe(III)(Por) to Fe(IV)=O(Por(·+)) in human heme oxygenase isoform-1 (hHO-1) and the structurally homologous protein from Corynebacterium diphtheriae (cdHO). Site-directed mutagenesis on hHO-1 probes the reduction of Fe(IV)=O(Por(·+)) by tyrosine residues within 11 Å of the prosthetic group. In hHO-1, Y58· is implicated as the most likely site of oxidation, based on the pH and pD dependent kinetics. The absence of solvent deuterium isotope effects in basic solutions of hHO-1 and cdHO contrasts with the behavior of these proteins in the acidic solution, suggesting that long-range proton-coupled electron transfer predominates over electron transfer. PMID:25023856

  13. Investigating protein conformational energy landscapes and atomic resolution dynamics from NMR dipolar couplings: a review

    NASA Astrophysics Data System (ADS)

    Salmon, Loïc; Blackledge, Martin

    2015-12-01

    Nuclear magnetic resonance spectroscopy is exquisitely sensitive to protein dynamics. In particular inter-nuclear dipolar couplings, that become measurable in solution when the protein is dissolved in a dilute liquid crystalline solution, report on all conformations sampled up to millisecond timescales. As such they provide the opportunity to describe the Boltzmann distribution present in solution at atomic resolution, and thereby to map the conformational energy landscape in unprecedented detail. The development of analytical methods and approaches based on numerical simulation and their application to numerous biologically important systems is presented.

  14. Orotate phosphoribosyltransferase from baker's yeast: I. Kinetic analysis, chemical modification, and proton NMR spectroscopy of the enzyme substrate complex. II. Amino acid analysis and NMR spectroscopy of the protein

    SciTech Connect

    Strauss, R.S.

    1986-01-01

    Kinetic analysis of the effect of pH on the reversible reaction catalyzed by orotate phosphoribosyltransferase (OPRTase) from Baker's yeast revealed that different amino acid residues may enable the enzyme-catalyzed reactions to proceed in the forward and reverse directions, respectively. For the forward reaction, there appear to be at least two critical amino acid residues (pK's 4.6 and 7.1) which must be in a deprotonated state to reach a maximum activity near pH 8 which is maintained through pH 9.5. For the reverse reaction, maximum activity is reached near pH 7 (pK's at 5.4) and then the activity decreases at higher pH (pK's at 7.9 and possibly above 9). A theoretical proton NMR spectrum was generated for OPRTase, based on its amino acid composition. The spectrum thus produced has a similar number of major peaks to that of the actual spectrum taken at 300 MHz. Spectra collected at various pH values between 8 and 5, were consistent with the maintenance of the gross conformational structure of the enzyme over that pH range.

  15. Magic-angle-spinning NMR of the drug resistant S31N M2 proton transporter from influenza A.

    PubMed

    Andreas, Loren B; Eddy, Matthew T; Chou, James J; Griffin, Robert G

    2012-05-01

    We report chemical shift assignments of the drug-resistant S31N mutant of M2(18-60) determined using 3D magic-angle-spinning (MAS) NMR spectra acquired with a (15)N-(13)C ZF-TEDOR transfer followed by (13)C-(13)C mixing by RFDR. The MAS spectra reveal two sets of resonances, indicating that the tetramer assembles as a dimer of dimers, similar to the wild-type channel. Helicies from the two sets of chemical shifts are shown to be in close proximity at residue H37, and the assignments reveal a difference in the helix torsion angles, as predicted by TALOS+, for the key resistance residue N31. In contrast to wild-type M2(18-60), chemical shift changes are minimal upon addition of the inhibitor rimantadine, suggesting that the drug does not bind to S31N M2. PMID:22480220

  16. Deciphering the Conformational Choreography of Zinc Coordination Complexes with Standard and Novel Proton NMR Techniques Combined with DFT Methods.

    PubMed

    Pucheta, Jose Enrique Herbert; Prim, Damien; Gillet, Jean Michel; Farjon, Jonathan

    2016-04-01

    The presence of water has been shown to deeply impact the stability and geometry of Zn complexes in solution. Evidence for tetra- and penta-coordinated species in a pyridylmethylamine-Zn(II) model complex is presented. Novel (1) H NMR tools such as T1 -filtered selective exchange spectroscopy and pure shifted gradient-encoded selective refocusing as well as classical 2D ((1) H-(1) H) exchange spectroscopy, diffusion-ordered spectroscopy and T1 ((1) H) measurements, in combination with density functional theory methods allow the full conformational dynamics of a pyridylmethylamine-Zn(II) complex to be revealed. Four conformers and two families of complexes depending on the hydration states are elucidated. PMID:26845749

  17. Proton NMR for detection, identification and quantification of adulterants in 160 herbal food supplements marketed for weight loss.

    PubMed

    Hachem, Rabab; Assemat, Gaëtan; Martins, Nathalie; Balayssac, Stéphane; Gilard, Véronique; Martino, Robert; Malet-Martino, Myriam

    2016-05-30

    One hundred and sixty food supplements (FS) marketed for weight loss and mainly purchased on the Internet were analyzed. All the FS were claimed as 100% natural containing only natural compounds, plant extracts and/or vitamins and the presence of an active pharmaceutical ingredient (API) was never mentioned. (1)H NMR spectroscopy was used for detecting the presence of adulterants and for their identification and quantification. Mass spectrometry was used as a complementary method for supporting their identification. Among the 164 samples considered because capsules from 5 different blisters of the same FS were analyzed, 56% were tainted with six API. Forty three contained sibutramine as single adulterant (26%), 9 phenolphthalein (6%) and 23 a mixture of these API (14%) that were both withdrawn from the market several years ago because of toxicity concerns. Sildenafil was found in 12 samples, either as a single adulterant (n=5) or in combination with sibutramine (n=3), phenolphthalein (n=3) and both sibutramine and phenolphthalein (n=1). Fluoxetine was present in 4 formulations, alone (n=3) or in combination with sibutramine and orlistat (n=1). At last, lorcaserine was detected in one FS. The content of sibutramine per dosage unit was comprised between 0.1 and 22 mg and that of phenolphthalein between 0.05 and 56 mg. The study also highlights poor manufacturing practices as evidenced for instance by the variability of API in capsules from different blisters of the same box. This paper demonstrates the need for more effective quality control of weight loss FS and the efficiency of (1)H NMR spectroscopy for the detection of tainted FS. PMID:26928212

  18. Kinetic coupling between electron and proton transfer in cytochrome c oxidase: simultaneous measurements of conductance and absorbance changes.

    PubMed Central

    Adelroth, P; Sigurdson, H; Hallén, S; Brzezinski, P

    1996-01-01

    Bovine heart cytochrome c oxidase is an electron-current driven proton pump. To investigate the mechanism by which this pump operates it is important to study individual electron- and proton-transfer reactions in the enzyme, and key reactions in which they are kinetically and thermodynamically coupled. In this work, we have simultaneously measured absorbance changes associated with electron-transfer reactions and conductance changes associated with protonation reactions following pulsed illumination of the photolabile complex of partly reduced bovine cytochrome c oxidase and carbon monoxide. Following CO dissociation, several kinetic phases in the absorbance changes were observed with time constants ranging from approximately 3 microseconds to several milliseconds, reflecting internal electron-transfer reactions within the enzyme. The data show that the rate of one of these electron-transfer reactions, from cytochrome a3 to a on a millisecond time scale, is controlled by a proton-transfer reaction. These results are discussed in terms of a model in which cytochrome a3 interacts electrostatically with a protonatable group, L, in the vicinity of the binuclear center, in equilibrium with the bulk through a proton-conducting pathway, which determines the rate of proton transfer (and indirectly also of electron transfer). The interaction energy of cytochrome a3 with L was determined independently from the pH dependence of the extent of the millisecond-electron transfer and the number of protons released, as determined from the conductance measurements. The magnitude of the interaction energy, 70 meV (1 eV = 1.602 x 10(-19) J), is consistent with a distance of 5-10 A between cytochrome a3 and L. Based on the recently determined high-resolution x-ray structures of bovine and a bacterial cytochrome c oxidase, possible candidates for L and a physiological role for L are discussed. PMID:8901574

  19. Multidrug Transport Protein NorM from Vibrio cholerae Simultaneously Couples to Sodium- and Proton-Motive Force*

    PubMed Central

    Jin, Yoonhee; Nair, Asha; van Veen, Hendrik W.

    2014-01-01

    Membrane transporters belonging to the multidrug and toxic compound extrusion family mediate the efflux of unrelated pharmaceuticals from the interior of the cell in organisms ranging from bacteria to human. These proteins are thought to fall into two classes that couple substrate efflux to the influx of either Na+ or H+. We studied the energetics of drug extrusion by NorM from Vibrio cholerae in proteoliposomes in which purified NorM protein was functionally reconstituted in an inside-out orientation. We establish that NorM simultaneously couples to the sodium-motive force and proton-motive force, and biochemically identify protein regions and residues that play important roles in Na+ or H+ binding. As the positions of protons are not available in current medium and high-resolution crystal structures of multidrug and toxic compound extrusion transporters, our findings add a previously unrecognized parameter to mechanistic models based of these structures. PMID:24711447

  20. On-shell coupled-channel approach to proton-hydrogen collisions without partial-wave expansion

    SciTech Connect

    Kadyrov, A. S.; Bray, I.; Stelbovics, A. T.

    2006-01-15

    A fully quantal approach to proton collisions with hydrogen based on the atomic-orbital close-coupling method is presented. The method leads to a system of coupled three-dimensional momentum-space integral equations for the scattering amplitudes. These equations are reduced to two-dimensional ones using an on-shell approximation. Furthermore, by considering the symmetry of the problem, we demonstrate that these can be reduced to just one dimension. The resulting equations are solved without partial-wave expansion. Cross sections for electron transfer in proton collisions with the ground state of atomic hydrogen are calculated and shown to agree well with experiment over a wide energy range.

  1. A non-Karplus effect: evidence from phosphorus heterocycles and DFT calculations of the dependence of vicinal phosphorus-hydrogen NMR coupling constants on lone-pair conformation.

    PubMed

    Hersh, William H; Lam, Sherrell T; Moskovic, Daniel J; Panagiotakis, Antonios J

    2012-06-01

    In contrast to literature reports of a Karplus-type curve that correlates (3)J(PH) with phosphorus-hydrogen dihedral angle, a recently reported glycine-derived 1,3,2-oxazaphospholidine (7c) has two hydrogen atoms on the ring with identical PNCH dihedral angles but measured coupling constants of ∼6 and 1.5 Hz. DFT calculations were in accord with these values and suggested that the smaller coupling constant is negative. Experimental evidence of the opposite signs of these coupling constants was obtained by analysis of the ABX NMR spectrum of the new glycine-derived N-p-toluenesulfonyl phosphorus heterocycle 6c. DFT calculations on 6c and on Me(2)NPCl(2) and t-BuPCl(2) were also in accord with NMR data and allowed confirmation of unusual features including a lone pair effect on (3)J(PH), the negative coupling constant, temperature-dependent chemical shifts due to rotation about the sulfonamide S-N bond, and vicinal phosphorus-hydrogen coupling constants over 40 Hz. Calculation of phosphorus-hydrogen coupling constants both as a function of PYCH dihedral angle θ (Y = O, N, C) and lone pair-PYC dihedral angle ω shows similar θ,ω surfaces for (3)J(PH) with a range of (3)J(PH) from -4.4 to +51 Hz and demonstrates the large non-Karplus effect of lone-pair conformation on vicinal phosphorus-hydrogen coupling constants. PMID:22612503

  2. A Non–Karplus Effect: Evidence from Phosphorus Heterocycles and DFT Calculations of the Dependence of Vicinal Phosphorus-Hydrogen NMR Coupling Constants on Lone-Pair Conformation

    PubMed Central

    Lam, Sherrell T.; Moskovic, Daniel J.; Panagiotakis, Antonios J.

    2012-01-01

    In contrast to literature reports of a Karplus-type curve that correlates 3JPH with phosphorus-hydrogen dihedral angle, a recently-reported glycine-derived 1,3,2-oxazaphospholidine (7c) has two hydrogen atoms on the ring with identical PNCH dihedral angles but measured coupling constants of ~6 Hz and 1.5 Hz. DFT calculations were in accord with these values, and suggested that the smaller coupling constant is negative. Experimental evidence of the opposite signs of these coupling constants was obtained by analysis of the ABX NMR spectrum of the new glycine-derived N-p-toluenesulfonyl phosphorus heterocycle 6c. DFT calculations on 6c and on Me2NPCl2 and t-BuPCl2 were also in accord with NMR data, and allowed confirmation of unusual features including a lone pair effect on 3JPH, the negative coupling constant, temperature-dependent chemical shifts due to rotation about the sulfonamide S-N bond, and vicinal phosphorus-hydrogen coupling constants over 40 Hz. Calculation of phosphorus-hydrogen coupling constants both as a function of PYCH dihedral angle θ(Y = O, N, C) and lone pair-PYC dihedral angle ω showed similar θ,ω surfaces for 3JPH with a range of 3JPH from −4.4 Hz to +51 Hz, and demonstrates the large non–Karplus effect of lone-pair conformation on vicinal phosphorus-hydrogen coupling constants. PMID:22612503

  3. Change of translational-rotational coupling in liquids revealed by field-cycling 1H NMR

    NASA Astrophysics Data System (ADS)

    Meier, R.; Schneider, E.; Rössler, E. A.

    2015-01-01

    Applying the field-cycling nuclear magnetic resonance technique, the frequency dependence of the 1H spin-lattice relaxation rate, R 1 ω = T1 - 1 ω , is measured for propylene glycol (PG) which is increasingly diluted with deuterated chloroform. A frequency range of 10 kHz-20 MHz and a broad temperature interval from 220 to about 100 K are covered. The results are compared to those of experiments, where glycerol and o-terphenyl are diluted with their deuterated counter-part. Reflecting intra- as well as intermolecular relaxation, the dispersion curves R 1 ω , x (x denotes mole fraction PG) allow to extract the rotational time constant τrot(T, x) and the self-diffusion coefficient D(T, x) in a single experiment. The Stokes-Einstein-Debye (SED) relation is tested in terms of the quantity D(T, x) τrot(T, x) which provides a measure of an effective hydrodynamic radius or equivalently of the spectral separation of the translational and the rotational relaxation contribution. In contrast to o-terphenyl, glycerol and PG show a spectral separation much larger than suggested by the SED relation. In the case of PG/chloroform mixtures, not only an acceleration of the PG dynamics is observed with increasing dilution but also the spectral separation of rotational and translational relaxation contributions continuously decreases. Finally, following a behavior similar to that of o-terphenyl already at about x = 0.6; i.e., while D(T, x) τrot(T, x) in the mixture is essentially temperature independent, it strongly increases with x signaling thus a change of translational-rotational coupling. This directly reflects the dissolution of the hydrogen-bond network and thus a change of solution structure.

  4. Delineating the extracellular water-accessible surface of the proton-coupled folate transporter.

    PubMed

    Duddempudi, Phaneendra Kumar; Goyal, Raman; Date, Swapneeta Sanjay; Jansen, Michaela

    2013-01-01

    The proton-coupled folate transporter (PCFT) was recently identified as the major uptake route for dietary folates in humans. The three-dimensional structure of PCFT and its detailed interplay with function remain to be determined. We screened the water-accessible extracellular surface of HsPCFT using the substituted-cysteine accessibility method, to investigate the boundaries between the water-accessible surface and inaccessible buried protein segments. Single-cysteines, engineered individually at 40 positions in a functional cysteine-less HsPCFT background construct, were probed for plasma-membrane expression in Xenopus oocytes with a bilayer-impermeant primary-amine-reactive biotinylating agent (sulfosuccinimidyl 6-(biotinamido) hexanoate), and additionally for water-accessibility of the respective engineered cysteine with the sulfhydryl-selective biotinylating agent 2-((biotinoyl)amino)ethyl methanethiosulfonate. The ratio between Cys-selective over amine-selective labeling was further used to evaluate three-dimensional models of HsPCFT generated by homology / threading modeling. The closest homologues of HsPCFT with a known experimentally-determined three-dimensional structure are all members of one of the largest membrane protein super-families, the major facilitator superfamily (MFS). The low sequence identity--14% or less--between HsPCFT and these templates necessitates experiment-based evaluation and model refinement of homology/threading models. With the present set of single-cysteine accessibilities, the models based on GlpT and PepTSt are most promising for further refinement. PMID:24205192

  5. Calcium-Mediated Regulation of Proton-Coupled Sodium Transport - Final Report

    SciTech Connect

    Schumaker, Karen S

    2013-10-24

    The long-term goal of our experiments was to understand mechanisms that regulate energy coupling by ion currents in plants. Activities of living organisms require chemical, mechanical, osmotic or electrical work, the energy for which is supplied by metabolism. Adenosine triphosphate (ATP) has long been recognized as the universal energy currency, with metabolism supporting the synthesis of ATP and the hydrolysis of ATP being used for the subsequent work. However, ATP is not the only energy currency in living organisms. A second and very different energy currency links metabolism to work by the movement of ions passing from one side of a membrane to the other. These ion currents play a major role in energy capture and they support a range of physiological processes from the active transport of nutrients to the spatial control of growth and development. In Arabidopsis thaliana (Arabidopsis), the activity of a plasma membrane Na+/H+ exchanger, SALT OVERLY SENSITIVE1 (SOS1), is essential for regulation of sodium ion homeostasis during plant growth in saline conditions. Mutations in SOS1 result in severely reduced seedling growth in the presence of salt compared to the growth of wild type. SOS1 is a secondary active transporter coupling movement of sodium ions out of the cell using energy stored in the transplasma membrane proton gradient, thereby preventing the build-up of toxic levels of sodium in the cytosol. SOS1 is regulated by complexes containing the SOS2 and CALCINEURIN B-LIKE10 (CBL10) or SOS3 proteins. CBL10 and SOS3 (also identified as CBL4) encode EF-hand calcium sensors that interact physically with and activate SOS2, a serine/threonine protein kinase. The CBL10/SOS2 or SOS3/SOS2 complexes then activate SOS1 Na+/H+ exchange activity. We completed our studies to understand how SOS1 activity is regulated. Specifically, we asked: (1) how does CBL10 regulate SOS1 activity? (2) What role do two putative CBL10-interacting proteins play in SOS1 regulation? (3) Are

  6. Proton-Coupled Electron Transfer Reactions at a Heme-Propionate in an Iron-Protoporphyrin-IX Model Compound

    PubMed Central

    2011-01-01

    A heme model system has been developed in which the heme-propionate is the only proton donating/accepting site, using protoporphyrin IX-monomethyl esters (PPIXMME) and N-methylimidazole (MeIm). Proton-coupled electron transfer (PCET) reactions of these model compounds have been examined in acetonitrile solvent. (PPIXMME)FeIII(MeIm)2-propionate (FeIII~CO2) is readily reduced by the ascorbate derivative 5,6-isopropylidine ascorbate to give (PPIXMME)FeII(MeIm)2-propionic acid (FeII~CO2H). Excess of the hydroxylamine TEMPOH or of hydroquinone similarly reduce FeIII~CO2, and TEMPO and benzoquinone oxidize FeII~CO2H to return to FeIII~CO2. The measured equilibrium constants, and the determined pKa and E1/2 values, indicate that FeII~CO2H has an effective bond dissociation free energy (BDFE) of 67.8 ± 0.6 kcal mol–1. In these PPIX models, electron transfer occurs at the iron center and proton transfer occurs at the remote heme propionate. According to thermochemical and other arguments, the TEMPOH reaction occurs by concerted proton-electron transfer (CPET), and a similar pathway is indicated for the ascorbate derivative. Based on these results, heme propionates should be considered as potential key components of PCET/CPET active sites in heme proteins. PMID:21524059

  7. Thermal hydraulic studies of spallation target for one-way coupled Indian accelerator driven systems with low energy proton beam

    NASA Astrophysics Data System (ADS)

    Mantha, V.; Mohanty, A. K.; Satyamurthy, P.

    2007-02-01

    BARC has recently proposed a one-way coupled ADS reactor. This reactor requires typically 1 GeV proton beam with 2 mA of current. Approximately 8 kW of heat is deposited in the window of the target. Circulating liquid metal target (lead/lead-bismuth{eutectic) has to extract this heat and this is a critical R&D problem to be solved. At present there are very few accelerators, which can give few mA and high-energy proton beam. However, accelerators with low energy and hundreds of micro-ampere current are commercially available. In view of this, it is proposed in this paper to simulate beam window heating of 8 kW in the target with low-energy proton beam. Detailed thermal analysis in the spallation and window region has been carried out to study the capability of heat extraction by circulating LBE for a typical target loop with a proton beam of 30 MeV energy and current of 0.267 mA. The heat deposition study is carried out using FLUKA code and flow analysis by CFD code. The detailed analysis of this work is presented in this paper.

  8. Ground-State Proton Transfer Kinetics in Green Fluorescent Protein

    PubMed Central

    2015-01-01

    Proton transfer plays an important role in the optical properties of green fluorescent protein (GFP). While much is known about excited-state proton transfer reactions (ESPT) in GFP occurring on ultrafast time scales, comparatively little is understood about the factors governing the rates and pathways of ground-state proton transfer. We have utilized a specific isotopic labeling strategy in combination with one-dimensional 13C nuclear magnetic resonance (NMR) spectroscopy to install and monitor a 13C directly adjacent to the GFP chromophore ionization site. The chemical shift of this probe is highly sensitive to the protonation state of the chromophore, and the resulting spectra reflect the thermodynamics and kinetics of the proton transfer in the NMR line shapes. This information is complemented by time-resolved NMR, fluorescence correlation spectroscopy, and steady-state absorbance and fluorescence measurements to provide a picture of chromophore ionization reactions spanning a wide time domain. Our findings indicate that proton transfer in GFP is described well by a two-site model in which the chromophore is energetically coupled to a secondary site, likely the terminal proton acceptor of ESPT, Glu222. Additionally, experiments on a selection of GFP circular permutants suggest an important role played by the structural dynamics of the seventh β-strand in gating proton transfer from bulk solution to the buried chromophore. PMID:25184668

  9. Total assignment and structure in solution of tetrandrine by NMR spectroscopy and molecular modelling

    NASA Astrophysics Data System (ADS)

    Thevand, André; Stanculescu, Ioana; Mandravel, Cristina; Woisel, Patrice; Surpateanu, Gheorghe

    2004-07-01

    High-resolution 1- and 2D NMR spectra of tetrandrine and molecular modelling were employed to characterise its structure in solution. Complete and unambiguous assignment of all proton and carbon resonance signals is reported. Scalar couplings were determined from dihedral angles with the Karplus equation. Inter-proton distances were evaluated from NOE correlation peaks. Comparison of simulated and X-ray conformations of tetrandrine reveals only small differences.

  10. Metal-free aqueous redox capacitor via proton rocking-chair system in an organic-based couple

    PubMed Central

    Tomai, Takaaki; Mitani, Satoshi; Komatsu, Daiki; Kawaguchi, Yuji; Honma, Itaru

    2014-01-01

    Safe and inexpensive energy storage devices with long cycle lifetimes and high power and energy densities are mandatory for the development of electrical power grids that connect with renewable energy sources. In this study, we demonstrated metal-free aqueous redox capacitors using couples comprising low-molecular-weight organic compounds. In addition to the electric double layer formation, proton insertion/extraction reactions between a couple consisting of inexpensive quinones/hydroquinones contributed to the energy storage. This energy storage mechanism, in which protons are shuttled back and forth between two electrodes upon charge and discharge, can be regarded as a proton rocking-chair system. The fabricated capacitor showed a large capacity (>20 Wh/kg), even in the applied potential range between 0–1 V, and high power capability (>5 A/g). The support of the organic compounds in nanoporous carbon facilitated the efficient use of the organic compounds with a lifetime of thousands of cycles. PMID:24395117

  11. Interrogation of the intersubunit interface of the open Hv1 proton channel with a probe of allosteric coupling

    PubMed Central

    Hong, Liang; Singh, Vikrant; Wulff, Heike; Tombola, Francesco

    2015-01-01

    The Hv1 voltage-gated proton channel is a dimeric complex consisting of two voltage-sensing domains (VSDs), each containing a gated proton permeation pathway. Dimerization is controlled by a cytoplasmic coiled-coil domain. The transitions from the closed to the open state in the two VSDs are known to occur cooperatively; however, the underlying mechanism is poorly understood. Intersubunit interfaces play a critical role in allosteric processes; but, such interfaces have not been determined in the open Hv1 channel. Here we show that 2-guanidinothiazole derivatives block the two Hv1 VSDs in a cooperative way, and use one of the compounds as a probe of allosteric coupling between open subunits. We find that the extracellular ends of the first transmembrane segments of the VSDs form the intersubunit interface that mediates coupling between binding sites, while the coiled-coil domain does not directly participate in the process. We also find strong evidence that the channel’s proton selectivity filter controls blocker binding cooperativity. PMID:26365828

  12. Conformational Analysis of a Dermatan Sulfate-Derived Tetrasaccharide by NMR, Molecular Modeling, and Residual Dipolar Couplings

    PubMed Central

    Silipo, Alba; Zhang, Zhenqing; Cañada, F. Javier; Molinaro, Antonio

    2014-01-01

    The solution conformation behavior of a dermatan-derived tetrasaccharide—ΔHexA-(1→3)-GalNAc4S-β-(1→4)-IdoA-α-(1→3)-red-GalNAc4S (S is a sulfate group)—has been explored by means of NMR spectroscopy, especially by NOE-based conformational analysis. The tetrasaccharide was present as four species, two of which are chemically different in the anomeric orientation of the reducing 2-deoxy-2-acetamido-galactose (red-GalNAc) residue, while the other two are the result of different conformations of the iduronic acid (IdoA) unit. The two α–-interconverting anomers were present in a 0.6:1 ratio. Ring conformations have been defined by analysis of 3JH,H coupling constants and interresidual NOE contacts. Both 2-deoxy-2-acetamido-galactose (GalNAc) residues were found in the 4C1 chair conformation, the unsaturated uronic acid (Δ-Hex A) adopts a strongly predominant half-chair 1H2 conformation, while the IdoA residue exists either in the 1C4 chair or in the 2S0 skewed boat geometries, in a 4:1 ratio. There is a moderate flexibility of Φ and Ψ torsions as suggested by nuclear Overhauser effects (NOEs), molecular modeling (MM), and molecular dynamics (MD) studies. This was further investigated by residual dipolar couplings (RDCs). One-bond C–H RDCs (1DC,H) and long-range H–H (3DH,H) RDCs were measured for the tetrasaccharide in a phage solution and interpreted in combination with restrained MD simulation. The RDC-derived data substantially confirmed the validity of the conformer distribution resulting from the NOE-derived simulations, but allowed an improved definition of the conformational behavior of the oligosaccharides in solution. In summary, the data show a moderate flexibility of the four tetrasaccharide species at the central glycosidic linkage. Differences in the shapes of species with the IdoA in skew and in chair conformations and in the distribution of the sulfate groups have also been highlighted. PMID:18072186

  13. Application of high-performance liquid chromatography-nuclear magnetic resonance coupling to the identification of limonoids from mahogany tree (Switenia macrophylla, Meliaceae) by stopped-flow 1D and 2D NMR spectroscopy.

    PubMed

    Schefer, Alexandre B; Braumann, Ulrich; Tseng, Li-Hong; Spraul, Manfred; Soares, Marisi G; Fernandes, João B; da Silva, Maria F G F; Vieira, Paulo C; Ferreira, Antonio G

    2006-09-22

    Separation and characterization of limonoids from Switenia macrophylla (Meliaceae) by HPLC-NMR technique has been described. Analyses were carried out using reversed-phase gradient HPLC elution coupled to NMR (600 MHz) spectrometer in stopped-flow mode. Separated peaks were collected into an interface unit prior to NMR measurements, which were performed with suppression of solvent signals by shaped pulses sequences. Structure elucidation of the limonoids was attained by data obtained from 1H NMR, TOCSY, gHSQC and gHMBC spectra without conventional isolation that is usually applied in natural products studies. PMID:16904679

  14. Measurements and coupled reaction channels analysis of one- and two-proton transfer reactions for the 28Si + 90,94Zr systems

    NASA Astrophysics Data System (ADS)

    Kalkal, Sunil; Mandal, S.; Jhingan, A.; Gehlot, J.; Sugathan, P.; Golda, K. S.; Madhavan, N.; Garg, Ritika; Goyal, Savi; Mohanto, Gayatri; Sandal, Rohit; Chakraborty, Santosh; Verma, Shashi; Behera, Bivash; Eleonora, G.; Wollersheim, H. J.; Singh, R.

    2012-03-01

    Measurements of angular distributions for one- and two-proton stripping reactions for 28Si + 90,94Zr systems were performed at 120 MeV. The experiment was carried out with the 28Si beam at Inter University Accelerator Center, New Delhi. The theoretical calculations were performed using the quantum mechanical coupled reaction channels code fresco. The distorted wave Born approximation calculations reproduced the experimental angular distributions for the one-proton transfer channel for both the systems reasonably well but failed for the two-proton transfer channel. Coupled channels calculations including various intermediate states (involving target and projectile inelastic excitations before and/or after transfer) along with the sequential transfer were able to reproduce the two-proton transfer angular distributions for both the systems reasonably well. It seems that at an energy above the Coulomb barrier, there is significant contribution of the indirect multistep and sequential transfer to the two-proton stripping reaction.

  15. NMR studies of the conformation of the natural sweetener rebaudioside A.

    PubMed

    Steinmetz, Wayne E; Lin, Alvin

    2009-12-14

    Rebaudioside A is a natural sweetener from Stevia rebaudiana in which four beta-D-glucopyranose units are attached to the aglycone steviol. Its (1)H and (13)C NMR spectra in pyridine-d(5) were assigned using 1D and 2D methods. Constrained molecular dynamics of solvated rebaudioside using NMR constraints derived from ROESY cross peaks yielded the orientation of the beta-D-glucopyranose units. Hydrogen bonding was examined using the temperature coefficients of the hydroxyl chemical shifts, ROESY and long-range COSY spectra, and proton-proton coupling constants. PMID:19889398

  16. The light magnet, coupling of electronic and nuclear angular momenta in optical NMR and ESR: Quantum theory

    NASA Astrophysics Data System (ADS)

    Evans, M. W.

    1992-07-01

    Optical NMR and ESR is a recently introduced technique in which a circularly polarized laser (a "light magnet") is used in an NMR or ESR spectrometer to induce magnetization. The spectral consequencies are developed with a quantum theory similar to the rigorous theory of Zeeman splitting of Russell-Saunders states, a theory which is suitable for atoms and molecules with net electronic angular momentum, and in which the antisymmetric electronic polarizability is finite. The optical NMR and ESR Hamiltonians are developed with the Wigner-Eckhart Theorem. The circularly polarized laser shifts the original NMR or ESR resonance lines, and splits the shifted lines into analytically useful patterns. The theory gives Landé factors which are in agreement with an earlier, simple, semiclassical theory ( J. Phys. Chem.95, 2256-2260 (1991)).

  17. A minimal non-supersymmetric S O(10) model: Gauge coupling unification, proton decay and fermion masses

    NASA Astrophysics Data System (ADS)

    Khan, Saki

    2016-06-01

    We present a minimal renormalizable non-supersymmetric S O(10) grand unified model with a symmetry breaking sector consisting of Higgs fields in the 54H + 126H + 10H representations. This model admits a single intermediate scale associated with Pati-Salam symmetry along with a discrete parity. Spontaneous symmetry breaking, the unification of gauge couplings and proton lifetime estimates are studied in detail in this framework. Including threshold corrections self-consistently, obtained from a full analysis of the Higgs potential, we show that the model is compatible with the current experimental bound on proton lifetime. The model generally predicts an upper bound of few times 1035 yrs for proton lifetime, which is not too far from the present Super-Kamiokande limit of τp ≳ 1.29 × 1034 yrs. With the help of a Pecci-Quinn symmetry and the resulting axion, the model provides a suitable dark matter candidate while also solving the strong CP problem. The intermediate scale, MI ≈ (1013 - 1014) GeV which is also the B - L scale, is of the right order for the right-handed neutrino mass which enables a successful description of light neutrino masses and oscillations. The Yukawa sector of the model consists of only two matrices in family space and leads to a predictive scenario for quark and lepton masses and mixings. The branching ratios for proton decay are calculable with the leading modes being p → e+π0 and p →v ¯π+ . Even though the model predicts no new physics within the reach of LHC, the next generation proton decay detectors and axion search experiments have the capability to pass verdict on this minimal scenario.

  18. The quantitative spectrum of inositol phosphate metabolites in avian erythrocytes, analysed by proton n.m.r. and h.p.l.c. with direct isomer detection.

    PubMed Central

    Radenberg, T; Scholz, P; Bergmann, G; Mayr, G W

    1989-01-01

    The spectrum of inositol phosphate isomers present in avian erythrocytes was investigated in qualitative and quantitative terms. Inositol phosphates were isolated in micromolar quantities from turkey blood by anion-exchange chromatography on Q-Sepharose and subjected to proton n.m.r. and h.p.l.c. analysis. We employed a h.p.l.c. technique with a novel, recently described complexometric post-column detection system, called 'metal-dye detection' [Mayr (1988) Biochem. J. 254, 585-591], which enabled us to identify non-radioactively labelled inositol phosphate isomers and to determine their masses. The results indicate that avian erythrocytes contain the same inositol phosphate isomers as mammalian cells. Denoted by the 'lowest-locant rule' [NC-IUB Recommendations (1988) Biochem. J. 258, 1-2] irrespective of true enantiomerism, these are Ins(1,4)P2, Ins(1,6)P2, Ins(1,3,4)P3, Ins(1,4,5)P3, Ins(1,3,4,5)P4, Ins(1,3,4,6)P4, Ins(1,4,5,6)P4, Ins(1,3,4,5,6)P5, and InsP6. Furthermore, we identified two inositol trisphosphate isomers hitherto not described for mammalian cells, namely Ins(1,5,6)P3 and Ins(2,4,5)P3. The possible position of these two isomers in inositol phosphate metabolism and implications resulting from absolute abundances of inositol phosphates are discussed. PMID:2604720

  19. Proton-coupled calcium transport by intact cells of Azotobacter vinelandii.

    PubMed

    Barnes, E M

    1980-08-01

    Addition of ionophores to resting aerobic cultures of Azotobacter vinelandii OP resulted in 45Ca2+ uptake (Km = 60 microM Ca2+; Vmax 1.1 nmol/min per mg of cell protein) which was inhibited by cations (La3+ greater than Mn2+ greater than Sr2+ greater Ba2+). The rate of Ca2+ entry correlated with the magnitude of a transmembrane proton gradient (inside acid) which developed in the respective order: valinomycin less than tetrachlorosalicylanilide less than nigericin less than gramicidin D less than tetrachlorosalicylanilide plus valinomycin. A process of calcium-proton exchange (antiport) is responsible for calcium accumulation under these conditions. PMID:6162836

  20. Slow magic-angle rotation 13C NMR studies of solid phosphonium iodides. The interplay of dipolar, shielding, and indirect coupling tensors

    NASA Astrophysics Data System (ADS)

    Harris, Robin K.; Packer, Kenneth J.; Thayer, Ann M.

    High-resolution 13C NMR spectra were recorded for solid [Me 2Ph 2P] +I - and [Me 3PhP] +I - using high-power decoupling, cross-polarization, and magic-angle rotation. Spectra of the ipso carbon, obtained with the nonquaternary suppression (dipolar dephasing) pulse sequence, show an unequal distribution intensity of spinning sidebands for the two peaks split by the isotropic coupling constant 1JPC. This effect is traced to the joint influence of (P, C) dipolar coupling and 13C shielding anisotropy. The existence of scalar coupling enables magic-angle rotation to distinguish the two subspectra which are present. Analysis of the sideband patterns yields values of the NMR parameters. Under certain assumptions, including that the axis of greatest shielding is perpendicular to the PC bond, it is shown that 1JPC is positive. In contrast to traditional methods of determining signs, this conclusion does not rely on knowledge of signs of other coupling constants.

  1. Photoregenerative I−/I3− couple as a liquid cathode for proton exchange membrane fuel cell

    PubMed Central

    Liu, Zhen; Wang, Yadong; Ai, Xinping; Tu, Wenmao; Pan, Mu

    2014-01-01

    A photoassisted oxygen reduction reaction (ORR) through I−/I3− redox couple was investigated for proton exchange membrane (PEM) fuel cell cathode reaction. The I−/I3−-based liquid cathode was used to replace conventional oxygen cathode, and its discharge product I− was regenerated to I3− by photocatalytic oxidation with the participation of oxygen. This new and innovative approach may provide a strategy to eliminate the usage of challenging ORR electrocatalysts, resulting in an avenue for developing low-cost and high-efficiency PEM fuel cells. PMID:25348812

  2. Revisiting NMR through-space J(FF) spin-spin coupling constants for getting insight into proximate F---F interactions.

    PubMed

    Contreras, Rubén H; Llorente, Tomás; Ducati, Lucas Colucci; Tormena, Cláudio Francisco

    2014-07-10

    At present times it is usual practice to mark biological compounds replacing an H for an F atom to study, by means of (19)F NMR spectroscopy, aspects such as binding sites and molecular folding features. This interesting methodology could nicely be improved if it is known how proximity interactions on the F atom affect its electronic structure as gauged through high-resolution (19)F NMR spectroscopy. This is the main aim of the present work and, to this end, differently substituted peri-difluoronaphthalenes are chosen as model systems. In such compounds are rationalized some interesting aspects of the diamagnetic and paramagnetic parts of the (19)F nuclear magnetic shielding tensor as well as the transmission mechanisms for the PSO and FC contributions to (4)JF1F8 indirect nuclear spin-spin coupling constants. PMID:24935717

  3. Use of an electrochemically-induced proton-coupled electron transfer reaction to control dimerization in a ureidopyrimidone 4 H-bond array.

    PubMed

    Clare, Laurie A; Smith, Diane K

    2016-06-01

    Cyclic voltammetric and spectroelectrochemical evidence is presented showing that the H-bonded dimer formed from a ureidopyrimidone derivative containing a phenylenediamine redox couple can be reversibly broken apart at mM concentrations in CH2Cl2 by an electrochemically induced proton-coupled electron transfer reaction. PMID:27227749

  4. Proton-coupled electron transfer: Metal hydrides find the sweet spot

    NASA Astrophysics Data System (ADS)

    Dempsey, Jillian L.

    2015-02-01

    The synchronous movement of protons and electrons orchestrated by enzymes gives rise to highly efficient catalytic processes in nature, such as photosynthesis. Now, researchers have choreographed similar reactivity for a metal hydride complex, setting the stage for efficient solar fuel production in artificial systems.

  5. Determination of NH proton chemical shift anisotropy with 14N-1H heteronuclear decoupling using ultrafast magic angle spinning solid-state NMR

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-12-01

    The extraction of chemical shift anisotropy (CSA) tensors of protons either directly bonded to 14N nuclei (I = 1) or lying in their vicinity using rotor-synchronous recoupling pulse sequence is always fraught with difficulty due to simultaneous recoupling of 14N-1H heteronuclear dipolar couplings and the lack of methods to efficiently decouple these interactions. This difficulty mainly arises from the presence of large 14N quadrupolar interactions in comparison to the rf field that can practically be achieved. In the present work it is demonstrated that the application of on-resonance 14N-1H decoupling with rf field strength ∼30 times weaker than the 14N quadrupolar coupling during 1H CSA recoupling under ultrafast MAS (90 kHz) results in CSA lineshapes that are free from any distortions from recoupled 14N-1H interactions. With the use of extensive numerical simulations we have shown the applicability of our proposed method on a naturally abundant L-Histidine HCl·H2O sample.

  6. Laser induced autofluorescence in the monitoring of β-mercaptoethanol mediated photo induced proton coupled electron transfer in proteins.

    PubMed

    Manjunath, S; Satish Rao, B S; Satyamoorthy, K; Mahato, K K

    2015-01-01

    Photo induced proton coupled electron transfer (PCET) is an important process that many organisms use for progression of catalytic reactions leading to energy conversion. In the present study, the influence of SDS and BME on the redox properties of tyrosine and tryptophan for five different globular proteins, BSA, HSA, RNase-A, trypsin and lysozyme were studied using laser induced autofluorescence. The proteins were subjected to denaturation under SDS, SDS plus heat and SDS plus β-mercaptoethanol (BME) plus heat and the corresponding fluorescence were recorded. The influence of BME on the autofluorescence properties of the proteins were evaluated upon tris-2-corboxy-ethyl phosphine (TCEP) denaturation. The BSA and HSA when exposed to SDS alone, exhibited hydrophobic collapse around their tryptophan moieties. However, these proteins when treated with SDS plus BME plus heat, an unusual red shift in the emission was observed, may be due to proton transfer from hydroxyl group of the excited tyrosine residues to the local microenvironments. The observation was further confirmed with similar proton transfer in absence of tryptophan in RNase-A showing involvement of tyrosine in the process. A drastic quenching of fluorescence in all of the proteins under study were also observed, may be due to photo-induced electron transfer (PET) from BME to the intrinsic fluorophores resulting in radical ions formation, evaluated upon DCFDA measurements. PMID:25985124

  7. Electrochemical proton-coupled electron transfer of an osmium aquo complex: theoretical analysis of asymmetric tafel plots and transfer coefficients.

    PubMed

    Ludlow, Michelle K; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2010-02-01

    Electrochemical proton-coupled electron transfer of an osmium aquo complex attached to a self-assembled monolayer on a gold electrode is studied with a recently developed theoretical formulation. The calculated hydrogen/deuterium kinetic isotope effect for the standard rate constant, the cathodic transfer coefficient at zero overpotential, and the Tafel plot are in excellent agreement with experimental data. The input quantities to the heterogeneous rate constant expressions were calculated with density functional theory in conjunction with dielectric continuum models, and no parameters were fit to experimental data. The theoretical calculations indicate that the asymmetry of the Tafel plot and the deviation of the transfer coefficient at zero overpotential from the standard value of one-half arise from the change in the equilibrium proton donor-acceptor distance upon electron transfer. The direction of the asymmetry and deviation from one-half is determined by the sign of this distance change, and the magnitude of these effects is determined by the magnitude of this distance change, as well as the reorganization energy and the distance dependence of the overlap between the initial and final proton vibrational wave functions. This theory provides experimentally testable predictions for the impact of specific system properties on the qualitative behavior of the Tafel plots. PMID:20067257

  8. Probing cation and vacancy ordering in the dry and hydrated yttrium-substituted BaSnO3 perovskite by NMR spectroscopy and first principles calculations: implications for proton mobility.

    PubMed

    Buannic, Lucienne; Blanc, Frédéric; Middlemiss, Derek S; Grey, Clare P

    2012-09-01

    Hydrated BaSn(1-x)Y(x)O(3-x/2) is a protonic conductor that, unlike many other related perovskites, shows high conductivity even at high substitution levels. A joint multinuclear NMR spectroscopy and density functional theory (total energy and GIPAW NMR calculations) investigation of BaSn(1-x)Y(x)O(3-x/2) (0.10 ≤ x ≤ 0.50) was performed to investigate cation ordering and the location of the oxygen vacancies in the dry material. The DFT energetics show that Y doping on the Sn site is favored over doping on the Ba site. The (119)Sn chemical shifts are sensitive to the number of neighboring Sn and Y cations, an experimental observation that is supported by the GIPAW calculations and that allows clustering to be monitored: Y substitution on the Sn sublattice is close to random up to x = 0.20, while at higher substitution levels, Y-O-Y linkages are avoided, leading, at x = 0.50, to strict Y-O-Sn alternation of B-site cations. These results are confirmed by the absence of a "Y-O-Y" (17)O resonance and supported by the (17)O NMR shift calculations. Although resonances due to six-coordinate Y cations were observed by (89)Y NMR, the agreement between the experimental and calculated shifts was poor. Five-coordinate Sn and Y sites (i.e., sites next to the vacancy) were observed by (119)Sn and (89)Y NMR, respectively, these sites disappearing on hydration. More five-coordinated Sn than five-coordinated Y sites are seen, even at x = 0.50, which is ascribed to the presence of residual Sn-O-Sn defects in the cation-ordered material and their ability to accommodate O vacancies. High-temperature (119)Sn NMR reveals that the O ions are mobile above 400 °C, oxygen mobility being required to hydrate these materials. The high protonic mobility, even in the high Y-content materials, is ascribed to the Y-O-Sn cation ordering, which prevents proton trapping on the more basic Y-O-Y sites. PMID:22691062

  9. Nonadiabatic dynamics of photoinduced proton-coupled electron transfer in a solvated phenol-amine complex.

    PubMed

    Goyal, Puja; Schwerdtfeger, Christine A; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2015-02-12

    Photoinduced concerted electron-proton transfer (EPT), denoted photo-EPT, is important for a wide range of energy conversion processes. Transient absorption and Raman spectroscopy experiments on the hydrogen-bonded p-nitrophenylphenol-t-butylamine complex, solvated in 1,2-dichloroethane, suggested that this complex may undergo photo-EPT. The experiments probed two excited electronic states that were interpreted as an intramolecular charge transfer (ICT) state and an EPT state. Herein mixed quantum mechanical/molecular mechanical nonadiabatic surface hopping dynamics is used to investigate the relaxation pathways following photoexcitation. The potential energy surface is generated on the fly with a semiempirical floating occupation molecular orbital complete active space configuration interaction method for the solute molecule and a molecular mechanical force field for the explicit solvent molecules. The free energy curves along the proton transfer coordinate illustrate that proton transfer is thermodynamically and kinetically favorable on the lower-energy excited state but not on the higher-energy excited state, supporting the characterization of these states as EPT and ICT, respectively. The nonadiabatic dynamics simulations indicate that the population decays from the ICT state to the EPT state in ∼100 fs and from the EPT state to the ground state on the slower time scale of ∼1 ps, qualitatively consistent with the experimental measurements. For ∼54% of the trajectories, the proton transfers from the phenol to the amine in ∼400 fs on the EPT state and then transfers back to the phenol rapidly upon decay to the ground state. Thus, these calculations augment the original interpretation of the experimental data by providing evidence of proton transfer on the EPT state prior to decay to the ground state. The fundamental insights obtained from these simulations are also relevant to other photo-EPT processes. PMID:25545667

  10. Neutron-Proton Coupling and the Lifetime of the First Excited State in ^16C

    NASA Astrophysics Data System (ADS)

    Fallon, Paul

    2008-04-01

    Nuclei near the valley of β-stability have strongly correlated proton and neutron spatial distributions. This need not be the case for nuclei with a large excess of one nucleon type and the search for new phenomena and structure effects due to the ``decoupling'' of neutrons and protons is of great interest in nuclear structure physics. Cited examples of decoupled behavior include neutron-halo nuclei with measurably different proton and neutron radial distributions, and low-energy dipole modes such as ``pygmy'' resonances where, simplistically, a core of equal numbers of protons and neutrons oscillates against the excess neutron ``skin'''. Recently, another example was suggested to occur in ^16C where the measurement of an anomalously quenched B(E2;2^+->^ 0^+) value of 0.63 e^2fm^4 combined with a large nuclear deformation led to the suggestion that the ^16C valence neutrons were decoupled from its near-spherical proton core (N.Imai et al., PRL 92 (2004) 062501; Z.Elekes et al., PLB 586 (2004) 34; H.J.Ong et al., PRC 73 (2006) 024610). In this talk I will discuss a new lifetime measurement for the first-excited 2^+ state in ^16C carried out at the LBNL 88-Inch Cyclotron using the Recoil Distance Method and ^9Be(^9Be,2p) fusion-evaporation reaction. The mean lifetime was found to be 11.7(20) ps corresponding to a B(E2) of 4.15(73) e^2fm^4, consistent with other even-even closed shell nuclei and neighboring systematics. Our result does not support the interpretation of decoupled protons and neutrons in ^16C. The revised value provides an important benchmark for theory. Time permitting I will present results on the neutron-rich nucleus ^30Ne produced in a 2p knockout reaction performed at the NSCL using the S800 spectrometer and SeGA gamma-ray detector. The measured (quenched) 2p knockout cross-section, when compared to theory, suggests a significant difference in the neutron intruder content between ^32Mg and ^30Ne, contrary to current shell models.

  11. Increased expression of the proton-sensing G protein-coupled receptor Gpr65 during retinal degeneration.

    PubMed

    Ail, D; Rüfenacht, V; Caprara, C; Samardzija, M; Kast, B; Grimm, C

    2015-08-20

    The retina is a metabolically highly active tissue that is sensitive to pH changes. Blinding diseases of the retina are often characterized by degeneration of photoreceptor cells altering the acid-base homeostasis of the tissue microenvironment and by an accompanying inflammatory response. GPR4, GPR65 and GPR68 are G protein-coupled receptors that aid cells to sense and survive conditions of acidic pH and inflammatory cells express Gpr65 enhancing their viability. Hence, we investigated expression and function of these proton-sensing GPRs in the normal and degenerating retina. We observed increased retinal expression of Gpr65, but not of Gpr4 and Gpr68, in mouse models of both inherited (rd10) and induced (light damage) retinal degeneration. Lack of GPR65 slightly accelerated photoreceptor degeneration in rd10 mice and resulted in a strong activation of microglia after light-injury. Since GPR65 was dispensable for normal retinal development, function and aging as evidenced by the evaluation of Gpr65(-/-) mice, our results indicate that the proton-sensing G protein-coupled receptor GPR65 may be involved in a mechanism that supports survival of photoreceptors in the degenerating retina. PMID:26117715

  12. Phase modulation in dipolar-coupled A 2 spin systems: effect of maximum state mixing in 1H NMR in vivo

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Coupling constants of nuclear spin systems can be determined from phase modulation of multiplet resonances. Strongly coupled systems such as citrate in prostatic tissue exhibit a more complex modulation than AX connectivities, because of substantial mixing of quantum states. An extreme limit is the coupling of n isochronous spins (A n system). It is observable only for directly connected spins like the methylene protons of creatine and phosphocreatine which experience residual dipolar coupling in intact muscle tissue in vivo. We will demonstrate that phase modulation of this "pseudo-strong" system is quite simple compared to those of AB systems. Theory predicts that the spin-echo experiment yields conditions as in the case of weak interactions, in particular, the phase modulation depends linearly on the line splitting and the echo time.

  13. Proton and deuterium NMR experiments in zero field. [Perdeuterated p-demethoxybenzene, perdeuterated malonic acid, diethyl terephthalate-d4, nonadecane-2,2'-D2, sodium propionate-D2

    SciTech Connect

    Millar, J.M.

    1986-02-01

    High field solid-state NMR lineshapes suffer from inhomogeneous broadening since resonance frequencies are a function of molecular orientation. Time domain zero field NMR is a two-dimensional field-cycling technique which removes this broadening by probing the evolution of the spin system under zero applied field. The simplest version, the sudden transition experiment, induces zero field evolution by the sudden removal of the applied magnetic field. Theory and experimental results of this experiment and several variations using pulsed dc magnetic fuelds to initiate zero field evolution are presented. In particular, the pulsed indirect detection method allows detection of the zero field spectrum of one nuclear spin species via another (usually protons) by utilizing the level crossings which occur upon adiabatic demagnetization to zero field. Experimental examples of proton/deuteron systems are presented which demonstrate the method results in enhanced sensitivity relative to that obtained in sudden transition experiments performed directly on deuterium. High resolution /sup 2/H NQR spectra of a series of benzoic acid derivatives are obtained using the sudden transition and indirect detection methods. Librational oscillations in the water molecules of barium chlorate monohydrate are studied using proton and deuterium ZF experiments. 177 refs., 88 figs., 2 tabs.

  14. Proton-Conducting Graphene Oxide-Coupled Neuron Transistors for Brain-Inspired Cognitive Systems.

    PubMed

    Wan, Chang Jin; Zhu, Li Qiang; Liu, Yang Hui; Feng, Ping; Liu, Zhao Ping; Cao, Hai Liang; Xiao, Peng; Shi, Yi; Wan, Qing

    2016-05-01

    Proton-conducting graphene oxide electrolyte films with very high electric-double-layer capacitance are used as the gate dielectrics for oxide-based neuron transistor fabrication. Paired-pulse facilitation, dendritic integration, and orientation tuning are successfully emulated. Additionally, neuronal gain controls (arithmetic) are also experimentally demonstrated. The results provide a new-concept approach for building brain-inspired cognitive systems. PMID:26972820

  15. Electrostatic effects on proton coupled electron transfer in oxomanganese complexes inspired by the oxygen-evolving complex of photosystem II.

    PubMed

    Amin, Muhamed; Vogt, Leslie; Vassiliev, Serguei; Rivalta, Ivan; Sultan, Mohammad M; Bruce, Doug; Brudvig, Gary W; Batista, Victor S; Gunner, M R

    2013-05-23

    The influence of electrostatic interactions on the free energy of proton coupled electron transfer in biomimetic oxomanganese complexes inspired by the oxygen-evolving complex (OEC) of photosystem II (PSII) are investigated. The reported study introduces an enhanced multiconformer continuum electrostatics (MCCE) model, parametrized at the density functional theory (DFT) level with a classical valence model for the oxomanganese core. The calculated pKa's and oxidation midpoint potentials (E(m)'s) match experimental values for eight complexes, indicating that purely electrostatic contributions account for most of the observed couplings between deprotonation and oxidation state transitions. We focus on pKa's of terminal water ligands in [Mn(II/III)(H2O)6](2+/3+) (1), [Mn(III)(P)(H2O)2](3-) (2, P = 5,10,15,20-tetrakis(2,6-dichloro-3-sulfonatophenyl)porphyrinato), [Mn2(IV,IV)(μ-O)2(terpy)2(H2O)2](4+) (3, terpy = 2,2':6',2″-terpyridine), and [Mn3(IV,IV,IV)(μ-O)4(phen)4(H2O)2](4+) (4, phen = 1,10-phenanthroline) and the pKa's of μ-oxo bridges and Mn E(m)'s in [Mn2(μ-O)2(bpy)4] (5, bpy = 2,2'-bipyridyl), [Mn2(μ-O)2(salpn)2] (6, salpn = N,N'-bis(salicylidene)-1,3-propanediamine), [Mn2(μ-O)2(3,5-di(Cl)-salpn)2] (7), and [Mn2(μ-O)2(3,5-di(NO2)-salpn)2] (8). The analysis of complexes 6-8 highlights the strong coupling between electron and proton transfers, with any Mn oxidation lowering the pKa of an oxo bridge by 10.5 ± 0.9 pH units. The model also accounts for changes in the E(m)'s by ligand substituents, such as found in complexes 6-8, due to the electron withdrawing Cl (7) and NO2 (8). The reported study provides the foundation for analysis of electrostatic effects in other oxomanganese complexes and metalloenzymes, where proton coupled electron transfer plays a fundamental role in redox-leveling mechanisms. PMID:23570540

  16. NMR Study of Strontium Binding by a Micaceous Mineral

    SciTech Connect

    Bowers, Geoffrey M.; Ravella, Ramesh; Komarneni, S.; Mueller, Karl T.

    2006-04-13

    The nature of strontium binding by soil minerals directly affects the transport and sequestration/remediation of radioactive strontium species released from leaking high-level nuclear waste storage tanks. However, the molecular-level structure of strontium binding sites has seldom been explored in phyllosilicate minerals by direct spectroscopic means and is not well-understood. In this work, we use solid-state NMR to analyze strontium directly and indirectly in a fully strontium-exchanged synthetic mica of nominal composition Na4Mg6Al4Si4O20F4. Thermogravimetric analysis, X-ray diffraction analysis, and NMR evidence supports that heat treatment at 500 °C for 4 h fully dehydrates the mica, creating a hydrogen-free interlayer. Analysis of the strontium NMR spectrum of the heat-treated mica shows a single strontium environment with a quadrupolar coupling constant of 9.02 MHz and a quadrupolar asymmetry parameter of 1.0. These quadrupolar parameters are consistent with a highly distorted and asymmetric coordination environment that would be produced by strontium cations without water in the coordination sphere bound deep within the ditrigonal holes. Evidence for at least one additional strontium environment, where proton-strontium couplings may occur, was found via a 1H-87Sr transfer of populations by double resonance NMR experiment. We conclude that the strontium cations in the proton-free interlayer are observable by 87Sr NMR and bound through electrostatic interactions as nine coordinate inner-sphere complexes sitting in the ditrigonal holes. Partially hydrated strontium cations invisible to direct 87Sr NMR are also present and located on the external mica surfaces, which are known to hydrate upon exposure to atmospheric moisture. These results demonstrate that modern pulsed NMR techniques and high fields can be used effectively to provide structural details of strontium binding by phyllosilicate minerals.

  17. An Integrated Laboratory Project in NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Hudson, Reggie L.; Pendley, Bradford D.

    1988-01-01

    Describes an advanced NMR project that can be done with a 60-MHz continuous-wave proton spectrometer. Points out the main purposes are to give students experience in second-order NMR analysis, the simplification of spectra by raising the frequency, and the effect of non-hydrogen nuclei on proton resonances. (MVL)

  18. Asymmetric protonation of EmrE.

    PubMed

    Morrison, Emma A; Robinson, Anne E; Liu, Yongjia; Henzler-Wildman, Katherine A

    2015-12-01

    The small multidrug resistance transporter EmrE is a homodimer that uses energy provided by the proton motive force to drive the efflux of drug substrates. The pKa values of its "active-site" residues--glutamate 14 (Glu14) from each subunit--must be poised around physiological pH values to efficiently couple proton import to drug export in vivo. To assess the protonation of EmrE, pH titrations were conducted with (1)H-(15)N TROSY-HSQC nuclear magnetic resonance (NMR) spectra. Analysis of these spectra indicates that the Glu14 residues have asymmetric pKa values of 7.0 ± 0.1 and 8.2 ± 0.3 at 45°C and 6.8 ± 0.1 and 8.5 ± 0.2 at 25°C. These pKa values are substantially increased compared with typical pKa values for solvent-exposed glutamates but are within the range of published Glu14 pKa values inferred from the pH dependence of substrate binding and transport assays. The active-site mutant, E14D-EmrE, has pKa values below the physiological pH range, consistent with its impaired transport activity. The NMR spectra demonstrate that the protonation states of the active-site Glu14 residues determine both the global structure and the rate of conformational exchange between inward- and outward-facing EmrE. Thus, the pKa values of the asymmetric active-site Glu14 residues are key for proper coupling of proton import to multidrug efflux. However, the results raise new questions regarding the coupling mechanism because they show that EmrE exists in a mixture of protonation states near neutral pH and can interconvert between inward- and outward-facing forms in multiple different protonation states. PMID:26573622

  19. Nonequilibrium Spin Dynamics: from Protons in Water to a Gauge Theory of Spin-Orbit Coupling

    NASA Astrophysics Data System (ADS)

    Tokatly, I. V.; Sherman, E. Ya.

    Nonequilibrium dynamics of spin degrees of freedom in condensed matter, ranging from classical liquids to solids and ultracold atomic gases, is one of the focus topics in physics. Here we present a gauge theory of spin dynamics in spinorbit coupled gases for a "pure" gauge realization of the spin-orbit coupling field. This approach allows one to describe the spin dynamics in fermionic systems in terms of exact general response functions and to map it on the density dynamics in a dual system without spin-orbit coupling. We apply this approach to electrons in disordered two-dimensional structures and to cold atomic gases of interacting fermions with synthetic spin-orbit coupling at very low temperatures.

  20. A Close Look at 13C CPMAS Linewidths in Solids for Rigid, Strongly Coupled Carbons under CW Proton Decoupling

    NASA Astrophysics Data System (ADS)

    VanderHart, D. L.; Campbell, G. C.

    1998-09-01

    Ambient-temperature13C linewidth (LW) and transverse relaxation (TC2) data are presented for the natural-abundance crystalline carbons of linear polyethylene (LPE) under CW proton decoupling conditions and magic angle spinning (MAS). This linewidth behavior typifies that seen for rigid methylene carbons whose attached protons are also strongly coupled to other protons. These data are presented for two LPE samples (unoriented, melt-crystallized and uniaxially oriented, extruded) as a function of several parameters including static field (1.4 T proton decoupling field strength (38 kHz < νH1< 90 kHz), MAS frequency (0.5 kHz < νr< 8 kHz) and RF frequency offsets from resonance (-4 kHz < Δνoff< 4 kHz). It is the ubiquitous nature of off-resonance proton irradiation (ORPI) (arising from fixed or rotationally dependent deviations from the true proton resonance condition) which provides the focus for this work. Corresponding contributions, LW(ORPI), to the total LW are treated within the general framework of the effective-field picture of CW decoupling. Then, considering the presence of spin fluctuations characteristic of the strongly-dipolar-coupled protons of LPE, LW(ORPI) can be traced to orbit-dependentTC2contributions to LW. Important dependences demonstrated and discussed include: (1) For "off-resonance" decoupling, there is a quadratic dependence of LW(ORPI) on (Δνoff/νH1)andthere is a strong dependence of the corresponding parabolic coefficient on νr. From the latter dependence, characteristic times for spin fluctuations are also estimated. (2) For "on-resonance" decoupling, LW(ORPI) is proportional to (νH1)-2andshows very little sensitivity to νr. These LW(ORPI) contributions become more important at higherB0since the principle reason for ORPI is the chemical shift anisotropy (CSA) of the13C-bonded protons. The difference in sensitivities of LW(ORPI) to νrfor the off-resonance and the on-resonance cases is traced back, respectively, to the

  1. SpinCouple: Development of a Web Tool for Analyzing Metabolite Mixtures via Two-Dimensional J-Resolved NMR Database.

    PubMed

    Kikuchi, Jun; Tsuboi, Yuuri; Komatsu, Keiko; Gomi, Masahiro; Chikayama, Eisuke; Date, Yasuhiro

    2016-01-01

    A new Web-based tool, SpinCouple, which is based on the accumulation of a two-dimensional (2D) (1)H-(1)H J-resolved NMR database from 598 metabolite standards, has been developed. The spectra include both J-coupling and (1)H chemical shift information; those are applicable to a wide array of spectral annotation, especially for metabolic mixture samples that are difficult to label through the attachment of (13)C isotopes. In addition, the user-friendly application includes an absolute-quantitative analysis tool. Good agreement was obtained between known concentrations of 20-metabolite mixtures versus the calibration curve-based quantification results obtained from 2D-Jres spectra. We have examined the web tool availability using nine series of biological extracts, obtained from animal gut and waste treatment microbiota, fish, and plant tissues. This web-based tool is publicly available via http://emar.riken.jp/spincpl. PMID:26624790

  2. Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation.

    PubMed

    Clore, G Marius; Kuszewski, John

    2003-02-12

    The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improvements in coordinate accuracy of NMR structures of RNA can be obtained by making use of two conformational database potentials of mean force: a nucleic acid torsion angle database potential consisting of various multidimensional torsion angle correlations; and an RNA specific base-base positioning potential that provides a simple geometric, statistically based, description of sequential and nonsequential base-base interactions. The former is based on 416 nucleic acid crystal structures solved at a resolution of coupling data have been measured in solution. PMID:12568611

  3. Coupling of Li motion and structural distortions in olivine LiMnPO4 from 7Li and 31P NMR

    NASA Astrophysics Data System (ADS)

    Rudisch, Christian; Grafe, Hans-Joachim; Geck, Jochen; Partzsch, Sven; Zimmermann, M. v.; Wizent, Nadja; Klingeler, Rüdiger; Büchner, Bernd

    2013-08-01

    We present a detailed 7Li- and 31P-NMR study on single crystalline LiMnPO4 in the paramagnetic and antiferromagnetic phase (AFM, TN˜34 K). This allows us to determine the spin directions in the field-induced spin-flop phase. In addition, the anisotropic dipolar hyperfine coupling tensor of the 7Li and 31P nuclei is also fully determined by orientation and temperature-dependent NMR experiments and compared to the calculated values from crystal structure data. Deviations of the experimental values from the theoretical ones are discussed in terms of Mn disorder which is induced by Li disorder. In fact, the disorder in the Mn sublattice is directly revealed by diffuse x-ray scattering data. The present results provide experimental evidence for the Li diffusion strongly coupling to structural distortions within the MnPO4 host, which is expected to significantly affect the Li mobility as well as the performance of batteries based on this material.

  4. Proton-coupled electron transfers: pH-dependent driving forces? Fundamentals and artifacts.

    PubMed

    Bonin, Julien; Costentin, Cyrille; Robert, Marc; Routier, Mathilde; Savéant, Jean-Michel

    2013-09-25

    Besides its own interest, tryptophan oxidation by photogenerated Ru complexes is one of the several examples where concerted proton-electron transfer (CPET) to water as proton acceptor endowed with a pH-dependent driving force has been invoked to explain the data. Since this notion is contrary to the very basic principles of chemical physics, it was interesting to attempt uncovering the source of this contradiction with an easily accessible substrate. Careful examination of the oxidation of the tryptophan (ethyl ester derivative) bearing a NH3(+)/NH2 group showed that there is no trace of such an unconventional H2O-CPET with a pH-dependent driving force. The reaction mechanism simply consists, with both the NH3(+) acid and NH2 basic forms of the tryptophan derivative, in a rate-determining electron-transfer step followed by deprotonation steps. The same is true with the ethyl ester-methyl amide derivative of tryptophan, whose behavior is even simpler since the molecule does not bear an acid-base group. No such unconventional H2O-CPET was found with phenol, another easily accessible substrate. It may thus be inferred that the same applies to less easily available systems in which electron transfer occurs intramolecularly. These observations help to rid the road of such artificial obstacles and improve present models of H2O-CPET reactions, a landmark towards the understanding of the role of water chains in natural systems. PMID:23972082

  5. Inorganic proton conducting electrolyte coupled oxide-based dendritic transistors for synaptic electronics

    NASA Astrophysics Data System (ADS)

    Wan, Chang Jin; Zhu, Li Qiang; Zhou, Ju Mei; Shi, Yi; Wan, Qing

    2014-04-01

    Ionic/electronic hybrid devices with synaptic functions are considered to be the essential building blocks for neuromorphic systems and brain-inspired computing. Here, artificial synapses based on indium-zinc-oxide (IZO) transistors gated by nanogranular SiO2 proton-conducting electrolyte films are fabricated on glass substrates. Spike-timing dependent plasticity and paired-pulse facilitation are successfully mimicked in an individual bottom-gate transistor. Most importantly, dynamic logic and dendritic integration established by spatiotemporally correlated spikes are also mimicked in dendritic transistors with two in-plane gates as the presynaptic input terminals.Ionic/electronic hybrid devices with synaptic functions are considered to be the essential building blocks for neuromorphic systems and brain-inspired computing. Here, artificial synapses based on indium-zinc-oxide (IZO) transistors gated by nanogranular SiO2 proton-conducting electrolyte films are fabricated on glass substrates. Spike-timing dependent plasticity and paired-pulse facilitation are successfully mimicked in an individual bottom-gate transistor. Most importantly, dynamic logic and dendritic integration established by spatiotemporally correlated spikes are also mimicked in dendritic transistors with two in-plane gates as the presynaptic input terminals. Electronic supplementary information (ESI) available: The structures and transfer characteristics of the IZO junctionless transistor working in bottom-gate mode and in-plane gate mode. See DOI: 10.1039/c3nr05882d

  6. Molecular characterization of dissolved organic matter in glacial ice: coupling natural abundance 1H NMR and fluorescence spectroscopy.

    PubMed

    Pautler, Brent G; Woods, Gwen C; Dubnick, Ashley; Simpson, André J; Sharp, Martin J; Fitzsimons, Sean J; Simpson, Myrna J

    2012-04-01

    Glaciers and ice sheets are the second largest freshwater reservoir in the global hydrologic cycle, and the onset of global climate warming has necessitated an assessment of their contributions to sea-level rise and the potential release of nutrients to nearby aquatic environments. In particular, the release of dissolved organic matter (DOM) from glacier melt could stimulate microbial activity in both glacial ecosystems and adjacent watersheds, but this would largely depend on the composition of the material released. Using fluorescence and (1)H NMR spectroscopy, we characterize DOM at its natural abundance in unaltered samples from a number of glaciers that differ in geographic location, thermal regime, and sample depth. Parallel factor analysis (PARAFAC) modeling of DOM fluorophores identifies components in the ice that are predominantly proteinaceous in character, while (1)H NMR spectroscopy reveals a mixture of small molecules that likely originate from native microbes. Spectrofluorescence also reveals a terrestrial contribution that was below the detection limits of NMR; however, (1)H nuclei from levoglucosan was identified in Arctic glacier ice samples. This study suggests that the bulk of the DOM from these glaciers is a mixture of biologically labile molecules derived from microbes. PMID:22385100

  7. Weak-coupling structure of proton resonant states in 23Al studied with RI beam at CNS

    NASA Astrophysics Data System (ADS)

    He, J. J.; Kubono, S.; Teranishi, T.; Notani, M.; Michimasa, S.; Baba, H.; Nishimura, S.; Nishimura, M.; Yanagisawa, Y.; Hokoiwa, N.; Kibe, M.; Gono, Y.; Moon, J. Y.; Lee, J. H.; Lee, C. S.; Iwasaki, H.; Kato, S.

    2006-07-01

    Proton resonances in 23Al have been investigated for the first time by the resonant elastic and inelastic scattering of 22Mg+p by using a 4.38 MeV/nucleon 22Mg beam bombarding a thick Hydrogen target. The low-energy 22Mg beam was separated by the CNS radioactive ion beam separator (CRIB). A new resonant state due to elastic scattering was observed at Ex = 3.00 MeV with a Jπ = (3/2+) assignment. Other three excited states due to resonant inelastic scattering at 3.14, 3.26 and 3.95 MeV were identified and all mainly decay to the first excited state in 22Mg by the proton emissions. The newly observed 3.95-MeV state probably has a spin-parity of Jπ = (7/2+). The resonant properties were determined from an R-matrix analysis of the excitation functions. The weak-coupling structure in 23Al is discussed in conjunction with a shell-model calculation.

  8. Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB

    PubMed Central

    Eicher, Thomas; Seeger, Markus A; Anselmi, Claudio; Zhou, Wenchang; Brandstätter, Lorenz; Verrey, François; Diederichs, Kay; Faraldo-Gómez, José D; Pos, Klaas M

    2014-01-01

    Membrane transporters of the RND superfamily confer multidrug resistance to pathogenic bacteria, and are essential for cholesterol metabolism and embryonic development in humans. We use high-resolution X-ray crystallography and computational methods to delineate the mechanism of the homotrimeric RND-type proton/drug antiporter AcrB, the active component of the major efflux system AcrAB-TolC in Escherichia coli, and one most complex and intriguing membrane transporters known to date. Analysis of wildtype AcrB and four functionally-inactive variants reveals an unprecedented mechanism that involves two remote alternating-access conformational cycles within each protomer, namely one for protons in the transmembrane region and another for drugs in the periplasmic domain, 50 Å apart. Each of these cycles entails two distinct types of collective motions of two structural repeats, coupled by flanking α-helices that project from the membrane. Moreover, we rationalize how the cross-talk among protomers across the trimerization interface might lead to a more kinetically efficient efflux system. DOI: http://dx.doi.org/10.7554/eLife.03145.001 PMID:25248080

  9. Proton conducting sodium alginate electrolyte laterally coupled low-voltage oxide-based transistors

    NASA Astrophysics Data System (ADS)

    Liu, Yang Hui; Qiang Zhu, Li; Shi, Yi; Wan, Qing

    2014-03-01

    Solution-processed sodium alginate electrolyte film shows a high proton conductivity of ˜5.5 × 10-3 S/cm and a high lateral electric-double-layer (EDL) capacitance of ˜2.0 μF/cm2 at room temperature with a relative humidity of 57%. Low-voltage in-plane-gate indium-zinc-oxide-based EDL transistors laterally gated by sodium alginate electrolytes are fabricated on glass substrates. The field-effect mobility, current ON/OFF ratio, and subthreshold swing of such EDL transistors are estimated to be 4.2 cm2 V-1 s-1, 2.8 × 106, and 130 mV/decade, respectively. At last, a low-voltage driven resistor-load inverter is also demonstrated. Such in-plane-gate EDL transistors have potential applications in portable electronics and low-cost biosensors.

  10. UV-Induced Proton-Coupled Electron Transfer in Cyclic DNA Miniduplexes.

    PubMed

    Zhang, Yuyuan; Li, Xi-Bo; Fleming, Aaron M; Dood, Jordan; Beckstead, Ashley A; Orendt, Anita M; Burrows, Cynthia J; Kohler, Bern

    2016-06-15

    The excited-state dynamics of two cyclic DNA miniduplexes, each containing just two base pairs, are investigated using time-resolved infrared spectroscopy. As in longer DNA duplexes, intrastrand electron transfer induced by UV excitation triggers interstrand proton transfer in the alternating miniduplex containing two out-of-phase G·C base pairs. The resulting excited state decays on a time scale of several tens of picoseconds. This state is absent when one of the two G residues is substituted by 8-oxo-7,8-dihydroguanine, a modification that is suggested to disrupt base stacking, while maintaining base pairing. These findings demonstrate that a nucleobase tetramer arranged as two stacked base pairs accurately captures the interplay between intrastrand and interstrand decay channels. The similar signals seen in the miniduplexes and longer sequences suggest that excited states in the latter rapidly localize on two adjacent base pairs. PMID:27203223

  11. Proton-coupled self-assembly of a porphyrin-naphthalenediimide dyad.

    PubMed

    Tu, Siyu; Kim, Se Hye; Joseph, Jojo; Modarelli, David A; Parquette, Jon R

    2013-06-01

    The construction of an n-p heterojunction through the self-assembly of a dyad based on tetraphenylporphyrin (TPP) and 1,4,5,8-naphthalenedimide (NDI) (1) is described. Proton transfer from the lysine head group of 1 to the porphyrin ring occurs concomitantly with self-assembly into 1D nanorods in CHCl3. TEM and AFM studies showed that the nanorods are formed by the lateral and vertical fusion of multilameller vesicles into networks and hollow ribbons, respectively. These intermediate structures transitioned to nanorods over the course of 4-6 days. Time-resolved spectroscopy revealed that photoinduced charge separation occurs with rate constants that depend on the nature of the aggregation. PMID:23564748

  12. Measurements and coupled reaction channels analysis of one and two proton transfer reactions for 28Si+90,94Zr systems

    NASA Astrophysics Data System (ADS)

    Kalkal, Sunil; Mandal, S.; Jhingan, A.; Gehlot, J.; Sugathan, P.; Golda, K. S.; Madhavan, N.; Garg, Ritika; Goyal, Savi; Mohanto, Gayatri; Verma, S.; Sandal, Rohit; Behera, Bivash; Eleonora, G.; Wollersheim, H. J.; Singh, R.

    2011-10-01

    Measurements of angular distributions for one and two proton stripping reactions for 28Si+90,94Zr systems were performed at lab energy 120 MeV with 28Si beam at Inter University Accelerator Center, New Delhi. Theoretical calculations performed using the quantum mechanical coupled reaction channels code FRESCO (including various intermediate states involving target and projectile excitations before and/or after transfer along with sequential transfer) were able to reproduce one and two proton transfer angular distributions for both the systems reasonably well. It was found that the DWBA calculations could describe the one proton transfer data well for both the systems but failed to reproduce the angular distributions for two proton transfer channels. The present measurements underline the importance of sequential transfer at energies much above the Coulomb barrier. We had also performed transfer reaction measurements for these systems in the sub- and near barrier region using recoil mass separator.

  13. Moving NMR

    NASA Astrophysics Data System (ADS)

    Blümich, Bernhard; Casanova, Federico; Danieli, Ernesto; Gong, Qingxia; Greferath, Marcus; Haber, Agnes; Kolz, Jürgen; Perlo, Juan

    2008-12-01

    Initiated by the use of NMR for well logging, portable NMR instruments are being developed for a variety of novel applications in materials testing and process analysis and control. Open sensors enable non-destructive testing of large objects, and small, cup-size magnets become available for high throughput analysis by NMR relaxation and spectroscopy. Some recent developments of mobile NMR are reviewed which delineate the direction into which portable NMR is moving.

  14. Pseudo-scalar pi N coupling and relativistic proton-nucleus scattering

    NASA Technical Reports Server (NTRS)

    Gross, Franz; Maung, Khin Maung; Tjon, J. A.; Townsend, L. W.; Wallace, S. J.

    1988-01-01

    Relativistic p-Ca-40 elastic scattering observables are calculated using relativistic NN amplitudes obtained from the solution of a two-body relativistic equation in which one particle is kept on its mass-shell. Results at 200 MeV are presented for two sets of NN amplitudes, one with pure pseudo-vector coupling for the pion and another with a 25 percent admixture of pseudo-scaling coupling. Both give a very good fit to the positive energy on-shell NN data. Differences between the predictions of these two models (which are shown to be due only to the differences in their corresponding negative energy amplitudes) provide a measure of the uncertainty in contructing Dirac optical potentials from NN amplitudes.

  15. Automated protein fold determination using a minimal NMR constraint strategy

    PubMed Central

    Zheng, Deyou; Huang, Yuanpeng J.; Moseley, Hunter N.B.; Xiao, Rong; Aramini, James; Swapna, G.V.T.; Montelione, Gaetano T.

    2003-01-01

    Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium-accuracy protein backbone structures. Our strategy derives from ideas originally introduced by other groups for determining medium-accuracy NMR structures of large proteins using deuterated, 13C-, 15N-enriched protein samples with selective protonation of side-chain methyl groups (13CH3). Data collection includes acquiring NMR spectra for automatically determining assignments of backbone and side-chain 15N, HN resonances, and side-chain 13CH3 methyl resonances. These assignments are determined automatically by the program AutoAssign using backbone triple resonance NMR data, together with Spin System Type Assignment Constraints (STACs) derived from side-chain triple-resonance experiments. The program AutoStructure then derives conformational constraints using these chemical shifts, amide 1H/2H exchange, nuclear Overhauser effect spectroscopy (NOESY), and residual dipolar coupling data. The total time required for collecting such NMR data can potentially be as short as a few days. Here we demonstrate an integrated set of NMR software which can process these NMR spectra, carry out resonance assignments, interpret NOESY data, and generate medium-accuracy structures within a few days. The feasibility of this combined data collection and analysis strategy starting from raw NMR time domain data was illustrated by automatic analysis of a medium accuracy structure of the Z domain of Staphylococcal protein A. PMID:12761394

  16. NMR logging apparatus

    DOEpatents

    Walsh, David O; Turner, Peter

    2014-05-27

    Technologies including NMR logging apparatus and methods are disclosed. Example NMR logging apparatus may include surface instrumentation and one or more downhole probes configured to fit within an earth borehole. The surface instrumentation may comprise a power amplifier, which may be coupled to the downhole probes via one or more transmission lines, and a controller configured to cause the power amplifier to generate a NMR activating pulse or sequence of pulses. Impedance matching means may be configured to match an output impedance of the power amplifier through a transmission line to a load impedance of a downhole probe. Methods may include deploying the various elements of disclosed NMR logging apparatus and using the apparatus to perform NMR measurements.

  17. Silver and Gold NMR

    PubMed Central

    Zangger, Klaus

    1999-01-01

    Silver and gold, together with copper, form the transition metal group IB elements in the periodic table and possess very different nuclear magnetic resonance (NMR) spectroscopic properties. While there is only one gold isotope (197Au), which has a spin of 3/2 and therefore a quadrupole moment, silver occurs in two isotopic forms (109Ag and 109Au), both of which have a spin 1/2 and similar NMR spectroscopic properties. The unfavorable properties of gold have prevented its NMR spectroscopic investigation thus far. On the other hand, there are several reports of silver NMR. However, the low sensitivity of silver, combined with its long relaxation times have rendered the direct detection of silver possible only with concentrations greater than a few tenth molar. Reviewed here are the general limitations of silver NMR and some techniques to partially overcome these limitations, as well as a summary of currently available chemical shift and scalar coupling data on 109Ag. PMID:18475898

  18. Solar-Driven Water Oxidation and Decoupled Hydrogen Production Mediated by an Electron-Coupled-Proton Buffer.

    PubMed

    Bloor, Leanne G; Solarska, Renata; Bienkowski, Krzysztof; Kulesza, Pawel J; Augustynski, Jan; Symes, Mark D; Cronin, Leroy

    2016-06-01

    Solar-to-hydrogen photoelectrochemical cells (PECs) have been proposed as a means of converting sunlight into H2 fuel. However, in traditional PECs, the oxygen evolution reaction and the hydrogen evolution reaction are coupled, and so the rate of both of these is limited by the photocurrents that can be generated from the solar flux. This in turn leads to slow rates of gas evolution that favor crossover of H2 into the O2 stream and vice versa, even through ostensibly impermeable membranes such as Nafion. Herein, we show that the use of the electron-coupled-proton buffer (ECPB) H3PMo12O40 allows solar-driven O2 evolution from water to proceed at rates of over 1 mA cm(-2) on WO3 photoanodes without the need for any additional electrochemical bias. No H2 is produced in the PEC, and instead H3PMo12O40 is reduced to H5PMo12O40. If the reduced ECPB is subjected to a separate electrochemical reoxidation, then H2 is produced with full overall Faradaic efficiency. PMID:27159121

  19. Proton conducting sodium alginate electrolyte laterally coupled low-voltage oxide-based transistors

    SciTech Connect

    Liu, Yang Hui; Wan, Qing; Qiang Zhu, Li; Shi, Yi

    2014-03-31

    Solution-processed sodium alginate electrolyte film shows a high proton conductivity of ∼5.5 × 10{sup −3} S/cm and a high lateral electric-double-layer (EDL) capacitance of ∼2.0 μF/cm{sup 2} at room temperature with a relative humidity of 57%. Low-voltage in-plane-gate indium-zinc-oxide-based EDL transistors laterally gated by sodium alginate electrolytes are fabricated on glass substrates. The field-effect mobility, current ON/OFF ratio, and subthreshold swing of such EDL transistors are estimated to be 4.2 cm{sup 2} V{sup −1} s{sup −1}, 2.8 × 10{sup 6}, and 130 mV/decade, respectively. At last, a low-voltage driven resistor-load inverter is also demonstrated. Such in-plane-gate EDL transistors have potential applications in portable electronics and low-cost biosensors.

  20. Overexpression of a proton-coupled vacuolar glucose exporter impairs freezing tolerance and seed germination.

    PubMed

    Klemens, Patrick A W; Patzke, Kathrin; Trentmann, Oliver; Poschet, Gernot; Büttner, Michael; Schulz, Alexander; Marten, Irene; Hedrich, Rainer; Neuhaus, H Ekkehard

    2014-04-01

    Arabidopsis vacuoles harbor, besides sugar transporter of the TMT-type, an early response to dehydration like 6 (ERDL6) protein involved in glucose export into the cytosol. However, the mode of transport of ERDL6 and the plant's feedback to overexpression of its activity on essential properties such as, for example, seed germination or freezing tolerance, remain unexplored. Using patch-clamp studies on vacuoles expressing AtERDL6 we demonstrated directly that this carrier operates as a proton-driven glucose exporter. Overexpression of BvIMP, the closest sugar beet (Beta vulgaris) homolog to AtERDL6, in Arabidopsis leads surprisingly to impaired seed germination under both conditions, sugar application and low environmental temperatures, but not under standard conditions. Upon cold treatment, BvIMP overexpressor plants accumulated lower quantities of monosaccharides than the wild-type, a response in line with the reduced frost tolerance of the transgenic Arabidopsis plants, and the fact that cold temperatures inhibits BvIMP transcription in sugar beet leaves. With these findings we show that the tight control of vacuolar sugar import and export is a key requisite for cold tolerance and seed germination of plants. PMID:24329902

  1. Characterization of tea cultivated at four different altitudes using 1H NMR analysis coupled with multivariate statistics.

    PubMed

    Ohno, Akiko; Oka, Kitaro; Sakuma, Chiseko; Okuda, Haruhiro; Fukuhara, Kiyoshi

    2011-05-25

    The taste of black tea differs according to the different areas in which the tea is grown, even for the same species of tea. A combination of (1)H NMR spectroscopy and partial least-squares discriminate analysis (PLS-DA) was used to assess the quality differences of tea leaves from four cultivation areas with different elevations, RAN > 1800 m, UDA = 1200 m, MEDA = 600 m, and YATA < 300 m, in Sri Lanka. As a result of a statistical analysis, PLS-DA showed a separation between high- and low-quality black teas derived from the four different tea cultivation areas. RAN from the highest elevation showed characteristic trends in the levels of theaflavin and theaflavin 3,3'-digallate that were found only in RAN, and the levels of theanine and caffeine were higher, and the levels of thearubigins, especially thearubigin 3,3'-digallate, were lower in RAN than in UDA, MEDA, and YATA. The structures of these components were determined by 1D and 2D NMR analyses. These results demonstrate that this method can be used to evaluate black tea quality according to the chemical composition or metabolites, which are characteristic of the tea leaves cultivated in four regions with different elevations in Sri Lanka. PMID:21456619

  2. Conformation of succinic acid: its pH dependence by Licry-NMR analysis

    NASA Astrophysics Data System (ADS)

    Chidichimo, G.; Formoso, P.; Golemme, A.; Imbardelli, D.

    The conformations of fully protonated (H2SA), fully deprotonated (SA=) and monoprotonated (HSA-) succinic acid have been investigated by means of nuclear magnetic resonance spectroscopy in liquid crystal mesophases (Licry-NMR). H-H and 13C-H direct dipolar couplings have been determined by measuring 1H-NMR and 13C-NMR spectra from quaternary nematic-lyotropic solutions of myristyltrimethylammonium bromide (MTAB), decanol, deuterated water and succinic acid (in each of its three different protonated forms). Direct dipolar couplings have been used to investigate the conformational equilibrium of the molecule in its three different protonation forms. Data could be interpreted in terms of a single conformation for each of the investigated forms. The dihedral angle between the H3-C5'-C5 and the C5'-C5-H1 planes gradually increases when going from the fully protonated H2SA species to the SA= ions. Our findings are different from those obtained by other authors by analysis of Jij couplings. In that case an equilibrium conformation between the gauche and trans conformers had been obtained.

  3. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.

    PubMed

    Venditti, Vincenzo; Egner, Timothy K; Clore, G Marius

    2016-06-01

    Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (<50 kDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus. PMID:26739383

  4. Inductively coupled NMR probe for versatile dynamic nuclear polarization operation at 7 T: Observation of 61 ± 2% 1H polarization at 4 K

    NASA Astrophysics Data System (ADS)

    Siaw, Ting Ann; Walker, Shamon A.; Armstrong, Brandon D.; Han, Song-I.

    2012-08-01

    We have performed dynamic nuclear polarization (DNP) experiments at liquid helium temperatures using a low-power (<70 mW) solid-state diode microwave source at 200 GHz—the electron paramagnetic resonance frequency of stable radicals at 7 T. We employed a home-built Alderman-Grant probe for the detection of 1H NMR signal at 300 MHz, as such coils are well suited for higher frequency NMR detection. The Alderman-Grant coil is inductively coupled to the rest of the radiofrequency (rf) circuit, whose design allows probe components to be placed away from the sample area, and also enables easy switching of coils with different diameters and resonance frequencies. We have tested our DNP instrument on a frozen nitroxide model system consisting of 4-Amino TEMPO dissolved in a glycerol:water mixture. The largest nuclear spin polarization observed was 61 ± 2% with a sample containing 20 mM 4-Amino TEMPO dissolved in deuterated glycerol (d-glycerol):D2O:H2O (50:40:10), amounting to record polarization measured to date at an easily amenable temperature of 4 K.

  5. Non-adiabatic electron-proton couplings in H2 by floating Gaussian method

    NASA Astrophysics Data System (ADS)

    Ichikawa, Yuichi; Kato, Tsuyoshi; Yamanouchi, Kaoru

    2016-08-01

    Time-dependent electron-nuclear wave functions of H2 were described by the floating Gaussian method. The equations of motion for the parameters that specify the wave functions are explicitly derived. By the imaginary time propagation, the ground-state wave functions were obtained. Five high frequency components appearing in the Fourier transformed spectra of the squared inter-particle distances were ascribed to the motion of electrons, and the two lowest frequency components among the five were identified as those representing coupling of the motions of electrons and nuclei.

  6. The Protonation Site of para-Dimethylaminobenzoic Acid Using Atmospheric Pressure Ionization Methods

    NASA Astrophysics Data System (ADS)

    Chai, Yunfeng; Weng, Guofeng; Shen, Shanshan; Sun, Cuirong; Pan, Yuanjiang

    2015-04-01

    The protonation site of para-dimethylaminobenzoic acid ( p-DMABA) was investigated using atmospheric pressure ionization methods (ESI and APCI) coupled with collision-induced dissociation (CID), nuclear magnetic resonance (NMR), and computational chemistry. Theoretical calculations and NMR experiments indicate that the dimethyl amino group is the preferred site of protonation both in the gas phase and aqueous solution. Protonation of p-DMABA occurs at the nitrogen atom by ESI independent of the solvents and other operation conditions under typical thermodynamic control. However, APCI produces a mixture of the nitrogen- and carbonyl oxygen-protonated p-DMABA when aprotic organic solvents (acetonitrile, acetone, and tetrahydrofuran) are used, exhibiting evident kinetic characteristics of protonation. But using protic organic solvents (methanol, ethanol, and isopropanol) in APCI still leads to the formation of thermodynamically stable N-protonated p-DMABA. These structural assignments were based on the different CID behavior of the N- and O-protonated p-DMABA. The losses of methyl radical and water are the diagnostic fragmentations of the N- and O-protonated p-DMABA, respectively. In addition, the N-protonated p-DMABA is more stable than the O-protonated p-DMABA in CID revealed by energy resolved experiments and theoretical calculations.

  7. An efficient proton-coupled electron-transfer process during oxidation of ferulic acid by horseradish peroxidase: coming full cycle.

    PubMed

    Derat, Etienne; Shaik, Sason

    2006-10-25

    Quantum mechanics/molecular mechanics calculations were utilized to study the process of oxidation of a native substrate (ferulic acid) by the active species of horseradish peroxidase (Dunford, H. B. Heme Peroxidases; Wiley-VCH: New York, 1999), Compound I and Compound II, and the manner by which the enzyme returns to its resting state. The results match experimental findings and reveal additional novel features. The calculations demonstrate that both oxidation processes are initiated by a proton-coupled electron-transfer (PCET) step, in which the active species of the enzyme participate only as electron-transfer partners, while the entire proton-transfer event is being relayed from the substrate to and from the His42 residue by a water molecule (W402). The reason for the observed (Henriksen, A; Smith, A. T.; Gajhede, M. J. Biol. Chem. 1999, 274, 35005-35011) similar reactivities of Compound I and Compound II toward ferulic acid is that the reactive isomer of Compound II is the, hitherto unobserved, Por(*)(+)Fe(III)OH isomer that resembles Compound I. The PCET mechanism reveals that His42 and W402 are crucial moieties and they determine the function of the HRP enzyme and account for its ability to perform substrate oxidation (Poulos, T. L. Peroxidases and Cytochrome P450. In The Porphyrin Handbook; Kadish, K. M., Smith, K. M., Guilard, R., Eds.; Academic Press: New York, 2000; Vol. 4, pp 189). In view of the results, the possibility of manipulating substrate oxidation by magnetic fields is an intriguing possibility. PMID:17044722

  8. Investigations on the role of proton-coupled electron transfer in hydrogen activation by [FeFe]-hydrogenase.

    PubMed

    Mulder, David W; Ratzloff, Michael W; Bruschi, Maurizio; Greco, Claudio; Koonce, Evangeline; Peters, John W; King, Paul W

    2014-10-29

    Proton-coupled electron transfer (PCET) is a fundamental process at the core of oxidation-reduction reactions for energy conversion. The [FeFe]-hydrogenases catalyze the reversible activation of molecular H2 through a unique metallocofactor, the H-cluster, which is finely tuned by the surrounding protein environment to undergo fast PCET transitions. The correlation of electronic and structural transitions at the H-cluster with proton-transfer (PT) steps has not been well-resolved experimentally. Here, we explore how modification of the conserved PT network via a Cys → Ser substitution at position 169 proximal to the H-cluster of Chlamydomonas reinhardtii [FeFe]-hydrogenase (CrHydA1) affects the H-cluster using electron paramagnetic resonance (EPR) and Fourier transform infrared (FTIR) spectroscopy. Despite a substantial decrease in catalytic activity, the EPR and FTIR spectra reveal different H-cluster catalytic states under reducing and oxidizing conditions. Under H2 or sodium dithionite reductive treatments, the EPR spectra show signals that are consistent with a reduced [4Fe-4S]H(+) subcluster. The FTIR spectra showed upshifts of νCO modes to energies that are consistent with an increase in oxidation state of the [2Fe]H subcluster, which was corroborated by DFT analysis. In contrast to the case for wild-type CrHydA1, spectra associated with Hred and Hsred states are less populated in the Cys → Ser variant, demonstrating that the exchange of -SH with -OH alters how the H-cluster equilibrates among different reduced states of the catalytic cycle under steady-state conditions. PMID:25286239

  9. pH-Dependent Reduction Potentials and Proton-Coupled Electron Transfer Mechanisms in Hydrogen-Producing Nickel Molecular Electrocatalysts

    SciTech Connect

    Horvath, Samantha; Fernandez, Laura; Appel, Aaron M.; Hammes-Schiffer, Sharon

    2013-04-01

    The nickel-based Ph Bz 2 2 P N electrocatalysts, which are comprised of a nickel atom and two 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane ligands, have been shown to effectively catalyze H2 production in acetonitrile. Recent electrochemical experiments revealed a linear dependence of the NiII/I reduction potential on pH, suggesting a proton-coupled electron transfer (PCET) reaction. In the proposed mechanism, the catalytic cycle begins with a PCET process involving electrochemical electron transfer to the nickel center and intermolecular proton transfer from an acid to the pendant amine ligand. This paper presents quantum mechanical calculations of this PCET process to examine the thermodynamics of the sequential mechanisms, in which either the electron or the proton transfers first (ET–PT and PT–ET, respectively), and the concerted mechanism (EPT). The favored mechanism depends on a balance among many factors, including the acid strength, association free energy for the acid–catalyst complex, PT free energy barrier, and ET reduction potential. The ET reduction potential is less negative after PT, favoring the PT–ET mechanism, and the association free energy is less positive after reduction, favoring the ET–PT mechanism. The calculations, along with analysis of the experimental data, indicate that the sequential ET–PT mechanism is favored for weak acids because of the substantial decrease in the association free energy after reduction. For strong acids, however, the PT–ET mechanism may be favored because the association free energy is somewhat smaller and PT is more thermodynamically favorable. The concerted mechanism could also occur, particularly for intermediate acid strengths. In the context of the entire catalytic cycle for H2 production, the initial PCET process involving intermolecular PT has a more negative reduction potential than the subsequent PCET process involving intramolecular PT. As a result, the second PCET should

  10. Structural evaluation of a novel pro-apoptotic peptide coupled to CNGRC tumor homing sequence by NMR.

    PubMed

    Sandoval, Cristina M; Geierstanger, Bernhard H; Fujimura, Satoshi; Balatbat, Calvin; Williams, Taylor; de Unamuno, Julio; Whiles-Lillig, Jennifer A; Ellerby, Lisa M; Ellerby, H Michael; Jennings, Patricia; Plesniak, Leigh A

    2006-06-01

    Hunter-killer peptides (HKPs) are synthetic peptides that target specific cell types for apoptosis. These studies report functional and structural characteristics of HKP9, an hunter-killer peptide that specifically targets tumor vasculature with a new apoptotic sequence. Vesicle leakage experiments were performed as a model for membrane perturbing activity. Placement of the homing sequence reduces both cell toxicity and vesicle leakage activity. NMR studies elucidate the conformation and orientation of HKP9 in micelles. The positively charged end of the HKP9 killing sequence is solvent exposed; however, the central portion of the peptide is helical and buried in dodecylphosphorylcholine micelles. The homing sequence is less solvent exposed than in a previously reported tumor-homing peptide. The results suggest that solvent accessibility of the homing sequence should be considered in design of future peptides. PMID:16882316

  11. Properties of the manganese(II) binding site in ternary complexes of Mnter dot ADP and Mnter dot ATP with chloroplast coupling factor 1: Magnetic field dependence of solvent sup 1 H and sup 2 H NMR relaxation rates

    SciTech Connect

    Haddy, A.E.; Frasch, W.D.; Sharp, R.R. )

    1989-05-02

    The influence of the binding of ADP and ATP on the high-affinity Mn(II) binding site of chloroplast coupling factor 1 (CF{sub 1}) was studied by analysis of field-dependent solvent proton and deuteron spin-lattice relaxation data. In order to characterize metal-nucleotide complexes of CF{sub 1} under conditions similar to those of the NMR experiments, the enzyme was analyzed for bound nucleotides and Mn(II) after incubation with AdN and MnCl{sub 2} and removal of labile ligands by extensive gel filtration chromatography. In the field-dependent NMR experiments, the Mn(II) binding site of CF{sub 1} was studied for three mole ratios of added Mn(II) to CF{sub 1}, 0.5, 1.0, and 1.5, in the presence of an excess of either ADP or ATP. The results were extrapolated to zero Mn(II) concentration to characterize the environment of the first Mn(II) binding site of Cf{sub 1}. In the presence of both adenine nucleotides, pronounced changes in the Mn(II) environment relative to that in Mn(II)-CF{sub 1} were evident; the local relaxation rate maxima were more pronounced and shifted to higher field strengths, and the relaxation rate per bound Mn(II) increased at all field strengths. Analysis of the data revealed that the number of exchangeable water molecules liganded to bound Mn(II) increased from one in the binary Mn(II)-CF{sub 1} complex to three and two in the ternary Mn(II)-ADP-CF{sub 1} and Mn(II)-ATP-CF{sub 1} complexes, respectively; these results suggest that a water ligand to bound Mn(II) in the Mn(II)-ADP-CF{sub 1} complex is replaced by the {gamma}-phosphate of ATP in the Mn(II)-ATP-CF{sub 1} complex. A binding model is presented to account for these observations.

  12. NMR Structure Determination for Larger Proteins Using Backbone-Only Data

    PubMed Central

    Raman, Srivatsan; Lange, Oliver F.; Rossi, Paolo; Tyka, Michael; Wang, Xu; Aramini, James; Liu, Gaohua; Ramelot, Theresa; Eletsky, Alexander; Szyperski, Thomas; Kennedy, Michael; Prestegard, James; Montelione, Gaetano T.; Baker, David

    2010-01-01

    Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-proton distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that structures can be accurately determined without NMR information on the sidechains for proteins up to 25 kDa by incorporating backbone chemical shifts, residual dipolar couplings, and amide proton distances into the Rosetta protein structure modelling methodology. These data, which are too sparse for conventional methods, serve only to guide conformational search towards the lowest energy conformations in the folding landscape; the details of the computed models are determined by the physical chemistry implicit in the Rosetta all atom energy function. The new method is not hindered by the deuteration required to suppress nuclear relaxation processes for proteins greater than 15 kDa, and should enable routine NMR structure determination for larger proteins. PMID:20133520

  13. Characterizing RNA ensembles from NMR data with kinematic models

    PubMed Central

    Fonseca, Rasmus; Pachov, Dimitar V.; Bernauer, Julie; van den Bedem, Henry

    2014-01-01

    Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

  14. Characterizing RNA ensembles from NMR data with kinematic models.

    PubMed

    Fonseca, Rasmus; Pachov, Dimitar V; Bernauer, Julie; van den Bedem, Henry

    2014-09-01

    Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem-loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

  15. Proton-Coupled Electron Transfer in a Series of Ruthenium-Linked Tyrosines with Internal Bases: Evaluation of a Tunneling Model for Experimental Temperature-Dependent Kinetics.

    PubMed

    Markle, Todd F; Zhang, Ming-Tian; Santoni, Marie-Pierre; Johannissen, Linus O; Hammarström, Leif

    2016-09-01

    Photoinitiated proton-coupled electron transfer (PCET) kinetics has been investigated in a series of four modified tyrosines linked to a ruthenium photosensitizer in acetonitrile, with each tyrosine bearing an internal hydrogen bond to a covalently linked pyridine or benzimidazole base. After correcting for differences in driving force, it is found that the intrinsic PCET rate constant still varies by 2 orders of magnitude. The differences in rates, as well as the magnitude of the kinetic isotope effect (KIE = kH/kD), both generally correlate with DFT calculated proton donor-acceptor distances. An Arrhenius analysis of temperature dependent data shows that the difference in reactivity arises primarily from differences in activation energies. We use this kinetic data to evaluate a commonly employed theoretical model for proton tunneling which includes a harmonic distribution of proton donor-acceptor distances due to vibrational motions of the molecule. Applying this model to the experimental data yields the conclusion that donor-acceptor compression is more facile in the compounds with shorter PT distance; however, this is contrary to independent calculations for the same compounds. This discrepancy is likely because the assumption in the model of Morse-shaped proton potential energy surfaces is inappropriate for (strongly) hydrogen-bonded systems. These results question the general applicability of this model. The results also suggest that a correlation of rate vs proton tunneling distance for the series of compounds is complicated by a concomitant variation of other relevant parameters. PMID:27490689

  16. Measurement of the inclusive 3-jet production differential cross section in proton-proton collisions at 7 TeV and determination of the strong coupling constant in the TeV range

    NASA Astrophysics Data System (ADS)

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, M.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Luyckx, S.; Ochesanu, S.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Zenoni, F.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Júnior, W. L. Aldá; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Martins, T. Dos Reis; Mora Herrera, C.; Pol, M. E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Tcholakov, V.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Tao, J.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Zou, W.; Avila, C.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Ellithi Kamel, A.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Paganini, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Bouvier, E.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Bagaturia, I.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Weber, M.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Heister, A.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Künsken, A.; Lingemann, J.; Nowack, A.; Nugent, I. M.; Perchalla, L.; Pooth, O.; Stahl, A.; Asin, I.; Bartosik, N.; Behr, J.; Behrenhoff, W.; Behrens, U.; Bell, A. J.; Bergholz, M.; Bethani, A.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Garcia, J. Garay; Geiser, A.; Gunnellini, P.; Hauk, J.; Hempel, M.; Horton, D.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Krücker, D.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Lutz, B.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Novgorodova, O.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Roland, B.; Ron, E.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schmidt, R.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Vargas Trevino, A. D. R.; Walsh, R.; Wissing, C.; Aldaya Martin, M.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Erfle, J.; Garutti, E.; Goebel, K.; Görner, M.; Haller, J.; Hoffmann, M.; Höing, R. S.; Kirschenmann, H.; Klanner, R.; Kogler, R.; Lange, J.; Lapsien, T.; Lenz, T.; Marchesini, I.; Ott, J.; Peiffer, T.; Pietsch, N.; Poehlsen, J.; Poehlsen, T.; Rathjens, D.; Sander, C.; Schettler, H.; Schleper, P.; Schlieckau, E.; Schmidt, A.; Seidel, M.; Sola, V.; Stadie, H.; Steinbrück, G.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Barth, C.; Baus, C.; Berger, J.; Böser, C.; Butz, E.; Chwalek, T.; De Boer, W.; Descroix, A.; Dierlamm, A.; Feindt, M.; Frensch, F.; Giffels, M.; Hartmann, F.; Hauth, T.; Husemann, U.; Katkov, I.; Kornmayer, A.; Kuznetsova, E.; Lobelle Pardo, P.; Mozer, M. U.; Müller, Th.; Nürnberg, A.; Quast, G.; Rabbertz, K.; Ratnikov, F.; Röcker, S.; Sieber, G.; Simonis, H. J.; Stober, F. M.; Ulrich, R.; Wagner-Kuhr, J.; Wayand, S.; Weiler, T.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Markou, A.; Markou, C.; Psallidas, A.; Topsis-Giotis, I.; Agapitos, A.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Stiliaris, E.; Aslanoglou, X.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Bencze, G.; Hajdu, C.; Hidas, P.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Molnar, J.; Palinkas, J.; Szillasi, Z.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Swain, S. K.; Beri, S. B.; Bhatnagar, V.; Gupta, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, M.; Kumar, R.; Mittal, M.; Nishu, N.; Singh, J. B.; Kumar, Ashok; Kumar, Arun; Ahuja, S.; Bhardwaj, A.; Choudhary, B. C.; Kumar, A.; Malhotra, S.; Naimuddin, M.; Ranjan, K.; Sharma, V.; Banerjee, S.; Bhattacharya, S.; Chatterjee, K.; Dutta, S.; Gomber, B.; Jain, Sa.; Jain, Sh.; Khurana, R.; Modak, A.; Mukherjee, S.; Roy, D.; Sarkar, S.; Sharan, M.; Abdulsalam, A.; Dutta, D.; Kailas, S.; Kumar, V.; Mohanty, A. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Banerjee, S.; Bhowmik, S.; Chatterjee, R. M.; Dewanjee, R. K.; Dugad, S.; Ganguly, S.; Ghosh, S.; Guchait, M.; Gurtu, A.; Kole, G.; Kumar, S.; Maity, M.; Majumder, G.; Mazumdar, K.; Mohanty, G. B.; Parida, B.; Sudhakar, K.; Wickramage, N.; Bakhshiansohi, H.; Behnamian, H.; Etesami, S. M.; Fahim, A.; Goldouzian, R.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Barbone, L.; Calabria, C.; Chhibra, S. S.; Colaleo, A.; Creanza, D.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Selvaggi, G.; Silvestris, L.; Venditti, R.; Zito, G.; Abbiendi, G.; Benvenuti, A. C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Primavera, F.; Rovelli, T.; Siroli, G. 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K.; Shrestha, S.; Skhirtladze, N.; Svintradze, I.; Gronberg, J.; Lange, D.; Rebassoo, F.; Wright, D.; Baden, A.; Belloni, A.; Calvert, B.; Eno, S. C.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kolberg, T.; Lu, Y.; Marionneau, M.; Mignerey, A. C.; Pedro, K.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Bauer, G.; Busza, W.; Cali, I. A.; Chan, M.; Di Matteo, L.; Dutta, V.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Ma, T.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Stöckli, F.; Sumorok, K.; Velicanu, D.; Veverka, J.; Wyslouch, B.; Yang, M.; Zanetti, M.; Zhukova, V.; Dahmes, B.; Gude, A.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Pastika, N.; Rusack, R.; Singovsky, A.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Gonzalez Suarez, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Malik, S.; Meier, F.; Snow, G. R.; Zvada, M.; Dolen, J.; Godshalk, A.; Iashvili, I.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Haley, J.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Trocino, D.; Wang, R. J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Velasco, M.; Won, S.; Brinkerhoff, A.; Chan, K. M.; Drozdetskiy, A.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Luo, W.; Lynch, S.; Marinelli, N.; Pearson, T.; Planer, M.; Ruchti, R.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Puigh, D.; Rodenburg, M.; Smith, G.; Winer, B. L.; Wolfe, H.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Brownson, E.; Mendez, H.; Ramirez Vargas, J. E.; Barnes, V. E.; Benedetti, D.; Bortoletto, D.; De Mattia, M.; Gutay, L.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Lopes Pegna, D.; Maroussov, V.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Yoo, H. D.; Zablocki, J.; Zheng, Y.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. M.; Geurts, F. J. M.; Li, W.; Michlin, B.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Khukhunaishvili, A.; Petrillo, G.; Vishnevskiy, D.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Lungu, G.; Mesropian, C.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Kaplan, S.; Lath, A.; Panwalkar, S.; Park, M.; Patel, R.; Salur, S.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Castaneda Hernandez, A.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Khotilovich, V.; Krutelyov, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Sakuma, T.; Suarez, I.; Tatarinov, A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kovitanggoon, K.; Kunori, S.; Lee, S. W.; Libeiro, T.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sharma, M.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Clarke, C.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Dodd, L.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Taylor, D.; Verwilligen, P.; Vuosalo, C.; Woods, N.; Collaboration, [Authorinst]The CMS

    2015-05-01

    This paper presents a measurement of the inclusive 3-jet production differential cross section at a proton-proton centre-of-mass energy of 7 TeV using data corresponding to an integrated luminosity of 5collected with the CMS detector. The analysis is based on the three jets with the highest transverse momenta. The cross section is measured as a function of the invariant mass of the three jets in a range of 445-3270 GeV and in two bins of the maximum rapidity of the jets up to a value of 2. A comparison between the measurement and the prediction from perturbative QCD at next-to-leading order is performed. Within uncertainties, data and theory are in agreement. The sensitivity of the observable to the strong coupling constant is studied. A fit to all data points with 3-jet masses larger than 664 GeV gives a value of the strong coupling constant of.

  17. Electron Transfer Reactivity of the Aqueous Iron(IV)-Oxo Complex. Outer-Sphere vs Proton-Coupled Electron Transfer.

    PubMed

    Bataineh, Hajem; Pestovsky, Oleg; Bakac, Andreja

    2016-07-01

    The kinetics of oxidation of organic and inorganic reductants by aqueous iron(IV) ions, Fe(IV)(H2O)5O(2+) (hereafter Fe(IV)aqO(2+)), are reported. The substrates examined include several water-soluble ferrocenes, hexachloroiridate(III), polypyridyl complexes M(NN)3(2+) (M = Os, Fe and Ru; NN = phenanthroline, bipyridine and derivatives), HABTS(-)/ABTS(2-), phenothiazines, Co(II)(dmgBF2)2, macrocyclic nickel(II) complexes, and aqueous cerium(III). Most of the reductants were oxidized cleanly to the corresponding one-electron oxidation products, with the exception of phenothiazines which produced the corresponding oxides in a single-step reaction, and polypyridyl complexes of Fe(II) and Ru(II) that generated ligand-modified products. Fe(IV)aqO(2+) oxidizes even Ce(III) (E(0) in 1 M HClO4 = 1.7 V) with a rate constant greater than 10(4) M(-1) s(-1). In 0.10 M aqueous HClO4 at 25 °C, the reactions of Os(phen)3(2+) (k = 2.5 × 10(5) M(-1) s(-1)), IrCl6(3-) (1.6 × 10(6)), ABTS(2-) (4.7 × 10(7)), and Fe(cp)(C5H4CH2OH) (6.4 × 10(7)) appear to take place by outer sphere electron transfer (OSET). The rate constants for the oxidation of Os(phen)3(2+) and of ferrocenes remained unchanged in the acidity range 0.05 < [H(+)] < 0.10 M, ruling out prior protonation of Fe(IV)aqO(2+) and further supporting the OSET assignment. A fit to Marcus cross-relation yielded a composite parameter (log k22 + E(0)Fe/0.059) = 17.2 ± 0.8, where k22 and E(0)Fe are the self-exchange rate constant and reduction potential, respectively, for the Fe(IV)aqO(2+)/Fe(III)aqO(+) couple. Comparison with literature work suggests k22 < 10(-5) M(-1) s(-1) and thus E(0)(Fe(IV)aqO(2+)/Fe(III)aqO(+)) > 1.3 V. For proton-coupled electron transfer, the reduction potential is estimated at E(0) (Fe(IV)aqO(2+), H(+)/Fe(III)aqOH(2+)) ≥ 1.95 V. PMID:27320290

  18. A General Assignment Method for Oriented Sample (OS) Solid-state NMR of Proteins Based on The Correlation of Resonances through Heteronuclear Dipolar Couplings in Samples Aligned Parallel and Perpendicular to the Magnetic Field

    PubMed Central

    Lu, George J.; Son, Woo Sung; Opella, Stanley J.

    2011-01-01

    A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly 15N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly 15N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. PMID:21316275

  19. Development and Characterization of NMR Measurements for Polymer Gel Dosimetry

    NASA Astrophysics Data System (ADS)

    Kwong, Zachary; Whitney, Heather

    2012-03-01

    Polymer gel dosimeters are systems of water, gelatin, and monomers which form polymers upon irradiation. The gelatin matrix retains dose distribution in 3D form, facilitating truly integrated measurements of complex dose plans for radiation therapy. Polymer gels have two proton pools coupled by exchange: free solvent protons and bound polymerized macromolecular protons. Measuring magnetization transfer (MT) and relaxation affords useful insights into particle rigidity and chemical exchange effects on relaxation in polymer gels. Polymer gel dose response has been previously quantified with several techniques, most often in terms of MRI parameters, usually at field strengths of 1.5 T and below. The research described here investigates the dose response of a revised MAGIC gel dosimeter via both high-field imaging and simpler nuclear magnetic resonance (NMR) spectroscopy. This includes both transverse and longitudinal relaxation rates (R2 and R1) and quantitative MT parameters. We investigated estimating polymer molecular weight for a given applied dose using the Rouse model and R2 data from the imaging study. Finally, we began development of NMR methods for studying dose response, requiring adaption of NMR experiments to accommodate for radiation damping.

  20. DUAL FREQUENCY RESONATOR FOR 1.2 GHZ EPR/16.2 MHZ NMR CO-IMAGING

    PubMed Central

    Petryakov, Sergey; Samouilov, Alexandre; Kesselring, Eric; Caia, George L.; Sun, Ziqi; Zweier, Jay L.

    2010-01-01

    The development of a dual frequency resonator that enables both EPR and proton NMR imaging within the same resonator, magnet and gradient system is described. A novel design allows the same resonator to perform both EPR and proton NMR operation without moving resonator cables or switches. The resonator is capable of working at frequencies of 16.18 MHz for proton NMR and 1.2 GHz for EPR and is optimized for isolated rat heart experiments, measuring 22 mm in inner diameter and 19 mm in length. In EPR mode, the resonator functions as a one loop two gap resonator, electrically coupled through a half wavelength inverter. In NMR mode, it functions a single turn coil. Using the same loop for both modalities maximizes filling factor at both frequencies. Placing the tuning and switching controls away from the resonator prevents any inadvertent movement that would cause errors of EPR and NMR co-imaging registration. The resonator enabled good quality EPR and proton MRI of isolated rat hearts with precise registration. PMID:20434379

  1. Coupled modeling of water transport and air-droplet interaction in the electrode of a proton exchange membrane fuel cell

    NASA Astrophysics Data System (ADS)

    Esposito, Angelo; Pianese, Cesare; Guezennec, Yann G.

    In this work, an accurate and computationally fast model for liquid water transport within a proton exchange membrane fuel cell (PEMFC) electrode is developed by lumping the space-dependence of the relevant variables. Capillarity is considered as the main transport mechanism within the gas diffusion layer (GDL). The novelty of the model lies in the coupled simulation of the water transport at the interface between gas diffusion layer and gas flow channel (GFC). This is achieved with a phenomenological description of the process that allows its simulation with relative simplicity. Moreover, a detailed two-dimensional visualization of such interface is achieved via geometric simulation of water droplets formation, growth, coalescence and detachment on the surface of the GDL. The model is useful for optimization analysis oriented to both PEMFC design and balance of plant. Furthermore, the accomplishment of reduced computational time and good accuracy makes the model suitable for control strategy implementation to ensure PEM fuel cells operation within optimal electrode water content.

  2. Electrochemical Electron Transfer and Proton-Coupled Electron Transfer: Effects of Double Layer and Ionic Environment on Solvent Reorganization Energies.

    PubMed

    Ghosh, Soumya; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2016-06-14

    Electron transfer and proton coupled electron transfer (PCET) reactions at electrochemical interfaces play an essential role in a broad range of energy conversion processes. The reorganization energy, which is a measure of the free-energy change associated with solute and solvent rearrangements, is a key quantity for calculating rate constants for these reactions. We present a computational method for including the effects of the double layer and ionic environment of the diffuse layer in calculations of electrochemical solvent reorganization energies. This approach incorporates an accurate electronic charge distribution of the solute within a molecular-shaped cavity in conjunction with a dielectric continuum treatment of the solvent, ions, and electrode using the integral equations formalism polarizable continuum model. The molecule-solvent boundary is treated explicitly, but the effects of the electrode-double layer and double layer-diffuse layer boundaries, as well as the effects of the ionic strength of the solvent, are included through an external Green's function. The calculated total reorganization energies agree well with experimentally measured values for a series of electrochemical systems, and the effects of including both the double layer and ionic environment are found to be very small. This general approach was also extended to electrochemical PCET and produced total reorganization energies in close agreement with experimental values for two experimentally studied PCET systems. PMID:27111050

  3. Proton echo-planar spectroscopic imaging of J-coupled resonances in human brain at 3 and 4 Tesla.

    PubMed

    Posse, Stefan; Otazo, Ricardo; Caprihan, Arvind; Bustillo, Juan; Chen, Hongji; Henry, Pierre-Gilles; Marjanska, Malgorzata; Gasparovic, Charles; Zuo, Chun; Magnotta, Vincent; Mueller, Bryon; Mullins, Paul; Renshaw, Perry; Ugurbil, Kamil; Lim, Kelvin O; Alger, Jeffry R

    2007-08-01

    In this multicenter study, 2D spatial mapping of J-coupled resonances at 3T and 4T was performed using short-TE (15 ms) proton echo-planar spectroscopic imaging (PEPSI). Water-suppressed (WS) data were acquired in 8.5 min with 1-cm(3) spatial resolution from a supraventricular axial slice. Optimized outer volume suppression (OVS) enabled mapping in close proximity to peripheral scalp regions. Constrained spectral fitting in reference to a non-WS (NWS) scan was performed with LCModel using correction for relaxation attenuation and partial-volume effects. The concentrations of total choline (tCho), creatine + phosphocreatine (Cr+PCr), glutamate (Glu), glutamate + glutamine (Glu+Gln), myo-inositol (Ins), NAA, NAA+NAAG, and two macromolecular resonances at 0.9 and 2.0 ppm were mapped with mean Cramer-Rao lower bounds (CRLBs) between 6% and 18% and approximately 150-cm(3) sensitive volumes. Aspartate, GABA, glutamine (Gln), glutathione (GSH), phosphoethanolamine (PE), and macromolecules (MMs) at 1.2 ppm were also mapped, although with larger mean CRLBs between 30% and 44%. The CRLBs at 4T were 19% lower on average as compared to 3T, consistent with a higher signal-to-noise ratio (SNR) and increased spectral resolution. Metabolite concentrations were in the ranges reported in previous studies. Glu concentration was significantly higher in gray matter (GM) compared to white matter (WM), as anticipated. The short acquisition time makes this methodology suitable for clinical studies. PMID:17610279

  4. Primary and secondary biomass burning aerosols determined by proton nuclear magnetic resonance (1H-NMR) spectroscopy during the 2008 EUCAARI campaign in the Po Valley (Italy)

    NASA Astrophysics Data System (ADS)

    Paglione, M.; Saarikoski, S.; Carbone, S.; Hillamo, R.; Facchini, M. C.; Finessi, E.; Giulianelli, L.; Carbone, C.; Fuzzi, S.; Moretti, F.; Tagliavini, E.; Swietlicki, E.; Eriksson Stenström, K.; Prévôt, A. S. H.; Massoli, P.; Canaragatna, M.; Worsnop, D.; Decesari, S.

    2014-05-01

    Atmospheric organic aerosols are generally classified as primary and secondary (POA and SOA) according to their formation processes. An actual separation, however, is challenging when the timescales of emission and gas-to-particle formation overlap. The presence of SOA formation in biomass burning plumes leads to scientific questions about whether the oxidized fraction of biomass burning aerosol is rather of secondary or primary origin, as some studies would suggest, and about the chemical compositions of oxidized biomass burning POA and SOA. In this study, we apply nuclear magnetic resonance (NMR) spectroscopy to investigate the functional group composition of fresh and aged biomass burning aerosols during an intensive field campaign in the Po Valley, Italy. The campaign was part of the EUCAARI project and was held at the rural station of San Pietro Capofiume in spring 2008. Factor analysis applied to the set of NMR spectra was used to apportion the wood burning contribution and other organic carbon (OC) source contributions, including aliphatic amines. Our NMR results, referred to the polar, water-soluble fraction of OC, show that fresh wood burning particles are composed of polyols and aromatic compounds, with a sharp resemblance to wood burning POA produced in wood stoves, while aged samples are clearly depleted of alcohols and are enriched in aliphatic acids with a smaller contribution of aromatic compounds. The comparison with biomass burning organic aerosols (BBOA) determined by high-resolution aerosol mass spectrometry (HR-TOF-AMS) at the site shows only a partial overlap between NMR BB-POA and AMS BBOA, which can be explained by either the inability of BBOA to capture all BB-POA composition, especially the alcohol fraction, or the fact that BBOA account for insoluble organic compounds unmeasured by the NMR. Therefore, an unambiguous composition for biomass burning POA could not be derived from this study, with NMR analysis indicating a higher O / C ratio

  5. Primary and secondary biomass burning aerosols determined by proton nuclear magnetic resonance (H-NMR) spectroscopy during the 2008 EUCAARI campaign in the Po Valley (Italy)

    NASA Astrophysics Data System (ADS)

    Paglione, M.; Saarikoski, S.; Carbone, S.; Hillamo, R.; Facchini, M. C.; Finessi, E.; Giulianelli, L.; Carbone, C.; Fuzzi, S.; Moretti, F.; Tagliavini, E.; Swietlicki, E.; Eriksson Stenström, K.; Prévôt, A. S. H.; Massoli, P.; Canaragatna, M.; Worsnop, D.; Decesari, S.

    2013-12-01

    Atmospheric organic aerosols are generally classified into primary and secondary (POA and SOA) according to their formation processes. An actual separation, however, is challenging when the timescales of emission and of gas-to-particle formation overlap. The presence of SOA formation in biomass burning plumes leads to scientific questions about whether the oxidized fraction of biomass burning aerosol is rather of secondary or primary origin, as some studies would suggest, and about the chemical compositions of oxidized biomass burning POA and SOA. In this study, we apply nuclear magnetic resonance (NMR) spectroscopy to investigate the functional group composition of fresh and aged biomass burning aerosols during an intensive field campaign in the Po Valley, Italy. The campaign was part of the EUCAARI project and was held at the rural station of San Pietro Capofiume in spring 2008. Factor analysis applied to the set of NMR spectra was used to apportion the wood burning contribution and other organic carbon (OC) source contributions, including aliphatic amines. Our NMR results, referred to the polar, water-soluble fraction of OC, show that fresh wood burning particles are composed of polyols and aromatic compounds, with a sharp resemblance with wood burning POA produced in wood stoves, while aged samples are clearly depleted of alcohols and are enriched in aliphatic acids with a smaller contribution of aromatic compounds. The comparison with biomass burning organic aerosols (BBOA) determined by high resolution aerosol mass spectrometry (HR-TOF-AMS) at the site shows only a partial overlap between NMR BB-POA and AMS BBOA, which can be explained by either the inability of BBOA to capture all BB-POA composition, especially the alcohol fraction, or the fact that BBOA account for insoluble organic compounds unmeasured by the NMR. Therefore, an unambiguous composition for biomass burning POA could not be derived from this study, with NMR analysis indicating a higher O / C

  6. Effect of J coupling on 1.3-ppm lipid methylene signal acquired with localised proton MRS at 3 T.

    PubMed

    Breitkreutz, Dylan Y; Fallone, B Gino; Yahya, Atiyah

    2015-10-01

    The purpose of this work was to investigate the effect of J-coupling interactions on the quantification and T2 determination of 1.3-ppm lipid methylene protons at 3 T. The response of the 1.3-ppm protons of hexanoic, heptanoic, octanoic, linoleic and oleic acid was measured as a function of point-resolved spectroscopy (PRESS) and stimulated echo acquisition mode (STEAM) TE. In addition, a narrow-bandwidth refocusing PRESS sequence designed to rewind J-coupling evolution of the 1.3-ppm protons was applied to the five fatty acids, to corn oil and to tibial bone marrow of six healthy volunteers. Peak areas were plotted as a function of TE, and data were fitted to monoexponentially decaying functions to determine Mo (the extrapolated area for TE = 0 ms) and T2 values. In phantoms, rewinding J-coupling evolution resulted in 198%, 64%, 44%, 20% and 15% higher T2 values for heptanoic, octanoic, linoleic and oleic acid, and corn oil, respectively, compared with those obtained with standard PRESS. The narrow-bandwidth PRESS sequence also resulted in significant changes in Mo , namely -77%, -22%, 28%, 23% and 28% for heptanoic, octanoic, linoleic and oleic acid, and corn oil, respectively. T2 values obtained with STEAM were closer to the values measured with narrow-bandwidth PRESS. On average, in tibial bone marrow (six volunteers) rewinding J-coupling evolution resulted in 21% ± 3% and 9 % ± 1% higher Mo and T2 values, respectively. This work demonstrates that the consequence of neglecting to consider scalar coupling effects on the quantification of 1.3-ppm lipid methylene protons and their T2 values is not negligible. The linoleic and oleic acid T2 results indicate that T2 measures of lipids with standard MRS techniques are dependent on lipid composition. PMID:26314546

  7. Recoupling of native homonuclear dipolar couplings in magic-angle-spinning solid-state NMR by the double-oscillating field technique

    NASA Astrophysics Data System (ADS)

    Straasø, Lasse Arnt; Nielsen, Niels Chr.

    2010-08-01

    A new solid-state NMR method, the double-oscillating field technique (DUO), that under magic-angle-spinning conditions produces an effective Hamiltonian proportional to the native high-field homonuclear dipole-dipole coupling operator is presented. The method exploits one part of the radio frequency (rf) field to recouple the dipolar coupling interaction with a relatively high scaling factor and to eliminate offset effects over a reasonable bandwidth while in the recoupling frame, the other part gives rise to a sufficiently large longitudinal component of the residual rf field that averages nonsecular terms and in addition ensures stability toward rf inhomogeneity and rf miscalibration. The capability of the DUO experiment to mediate transfer of polarization is described theoretically and compared numerically and experimentally with finite pulse rf driven recoupling and experimentally with dipolar-assisted rotational resonance. Two-dimensional recoupling experiments were performed on antiparallel amyloid fibrils of the decapeptide SNNFGAILSS with the FGAIL fragment uniformly labeled with C13 and N15.

  8. The metabolic profile of lemon juice by proton HR-MAS NMR: the case of the PGI Interdonato Lemon of Messina.

    PubMed

    Cicero, Nicola; Corsaro, Carmelo; Salvo, Andrea; Vasi, Sebastiano; Giofré, Salvatore V; Ferrantelli, Vincenzo; Di Stefano, Vita; Mallamace, Domenico; Dugo, Giacomo

    2015-01-01

    We have studied by means of High Resolution Magic Angle Spinning Nuclear Magnetic Resonance (HR-MAS NMR) the metabolic profile of the famous Sicilian lemon known as 'Interdonato Lemon of Messina PGI'. The PGI Interdonato Lemon of Messina possesses high organoleptic and healthy properties and is recognised as one of the most nutrient fruits. In particular, some of its constituents are actively studied for their chemo-preventive and therapeutic properties. In this paper, we have determined by means of HR-MAS NMR spectroscopy the molar concentration of the main metabolites constituent the juice of PGI Interdonato Lemon of Messina in comparison with that of the not-PGI Interdonato Lemon of Turkey. Our aim is to develop an analytical technique, in order to determine a metabolic fingerprint able to reveal commercial frauds in national and international markets. PMID:25702767

  9. Synthesis and physicochemical characterization of Gd-C4-thyroxin-DTPA, a potential MRI contrast agent. Evaluation of its affinity for human serum albumin by proton relaxometry, NMR diffusometry, and electrospray mass spectrometry.

    PubMed

    Henoumont, C; Vander Elst, L; Laurent, S; Muller, R N

    2010-03-18

    Gd-C(4)-thyroxin-DTPA, a potential MRI contrast agent, was synthesized from Gd-DTPA and thyroxine, which interacts strongly with human serum albumin (HSA). It was characterized in water by its relaxometric properties and its stability versus zinc transmetalation. The affinity of the complex for HSA was studied by using three different methods: proton relaxometry, NMR diffusometry, and electrospray mass spectrometry. From the results, it appears that Gd-C(4)-thyroxin-DTPA exhibits a relatively high relaxivity (r(1) = 9.01 s(-1) mM(-1) at 1.5 T and 310 K), a good stability versus zinc transmetalation, and a strong interaction with HSA (K(a) approximately 10,000 M(-1) with two binding sites). The kinetics of the exchange between the bound and the free form of the complex was evaluated by the NMR diffusometry technique. Competition experiments have allowed the assignment of the chelate's binding site on HSA. PMID:20175550

  10. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

    PubMed

    Salmon, Loïc; Giambaşu, George M; Nikolova, Evgenia N; Petzold, Katja; Bhattacharya, Akash; Case, David A; Al-Hashimi, Hashim M

    2015-10-14

    Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution. PMID:26306428

  11. Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.

    PubMed

    Yang, Shan; Al-Hashimi, Hashim M

    2015-07-30

    A growing number of studies employ time-averaged experimental data to determine dynamic ensembles of biomolecules. While it is well-known that different ensembles can satisfy experimental data to within error, the extent and nature of these degeneracies, and their impact on the accuracy of the ensemble determination remains poorly understood. Here, we use simulations and a recently introduced metric for assessing ensemble similarity to explore degeneracies in determining ensembles using NMR residual dipolar couplings (RDCs) with specific application to A-form helices in RNA. Various target ensembles were constructed representing different domain-domain orientational distributions that are confined to a topologically restricted (<10%) conformational space. Five independent sets of ensemble averaged RDCs were then computed for each target ensemble and a "sample and select" scheme used to identify degenerate ensembles that satisfy RDCs to within experimental uncertainty. We find that ensembles with different ensemble sizes and that can differ significantly from the target ensemble (by as much as ∑Ω ∼ 0.4 where ∑Ω varies between 0 and 1 for maximum and minimum ensemble similarity, respectively) can satisfy the ensemble averaged RDCs. These deviations increase with the number of unique conformers and breadth of the target distribution, and result in significant uncertainty in determining conformational entropy (as large as 5 kcal/mol at T = 298 K). Nevertheless, the RDC-degenerate ensembles are biased toward populated regions of the target ensemble, and capture other essential features of the distribution, including the shape. Our results identify ensemble size as a major source of uncertainty in determining ensembles and suggest that NMR interactions such as RDCs and spin relaxation, on their own, do not carry the necessary information needed to determine conformational entropy at a useful level of precision. The framework introduced here provides a general

  12. An NMR and relativistic DFT investigation of one-bond nuclear spin-spin coupling in solid triphenyl group-14 chlorides.

    PubMed

    Willans, Mathew J; Demko, Bryan A; Wasylishen, Roderick E

    2006-06-21

    A solid-state nuclear magnetic resonance and zeroth-order regular approximation density functional theory, ZORA-DFT, study of one-bond nuclear spin-spin coupling between group-14 nuclei and quadrupolar 35/37Cl nuclei in triphenyl group-14 chlorides, Ph3XCl (X = C, Si, Ge, Sn and Pb), is presented. This represents the first combined experimental and theoretical systematic study of spin-spin coupling involving spin-pairs containing quadrupolar nuclei. Solid-state NMR spectra have been acquired for all compounds in which X has a spin-1/2 isotope--13C, 29Si, [117/119]Sn and 207Pb-at applied magnetic fields of 4.70, 7.05 and 11.75 T. From simulations of these spectra, values describing the indirect spin-spin coupling tensor-the isotropic indirect spin-spin coupling constant, 1J(X, 35/37Cl)iso and the anisotropy of the J tensor, Delta1J(X, 35/37Cl)--have been determined for all but the lead-chlorine spin-pair. To better compare the indirect spin-spin coupling parameters between spin-pairs, 1J(iso) and Delta1J values were converted to their reduced coupling constants, 1K(iso) and Delta1K. From experiment, the sign of 1K(iso) was found to be negative while the sign of Delta1K is positive for all spin-pairs investigated. The magnitude of both 1K(iso) and Delta1K was found to increase as one moves down group-14. Theoretical values of the magnitude and sign of 1K(iso) and Delta1K were obtained from ZORA-DFT calculations and are in agreement with the available experimental data. From the calculations, the Fermi-contact mechanism was determined to provide the largest contribution to 1K(iso) for all spin-pairs while spin-dipolar and paramagnetic spin-orbit mechanisms make significant contributions to the anisotropy of K. The inclusion of relativistic effects was found to influence K(Sn,Cl) and K(Pb,Cl). PMID:16763706

  13. Roles of multiple-proton transfer pathways and proton-coupled electron transfer in the reactivity of the bis-FeIV state of MauG.

    PubMed

    Ma, Zhongxin; Williamson, Heather R; Davidson, Victor L

    2015-09-01

    The high-valent state of the diheme enzyme MauG exhibits charge-resonance (CR) stabilization in which the major species is a bis-Fe(IV) state with one heme present as Fe(IV)=O and the other as Fe(IV) with axial heme ligands provided by His and Tyr side chains. In the absence of its substrate, the high-valent state is relatively stable and returns to the diferric state over several minutes. It is shown that this process occurs in two phases. The first phase is redistribution of the resonance species that support the CR. The second phase is the loss of CR and reduction to the diferric state. Thermodynamic analysis revealed that the rates of the two phases exhibited different temperature dependencies and activation energies of 8.9 and 19.6 kcal/mol. The two phases exhibited kinetic solvent isotope effects of 2.5 and 2.3. Proton inventory plots of each reaction phase exhibited extreme curvature that could not be fit to models for one- or multiple-proton transfers in the transition state. Each did fit well to a model for two alternative pathways for proton transfer, each involving multiple protons. In each case the experimentally determined fractionation factors were consistent with one of the pathways involving tunneling. The percent of the reaction that involved the tunneling pathway differed for the two reaction phases. Using the crystal structure of MauG it was possible to propose proton-transfer pathways consistent with the experimental data using water molecules and amino acid side chains in the distal pocket of the high-spin heme. PMID:26283395

  14. Surface modification of Fe2TiO5 nanoparticles by silane coupling agent: Synthesis and application in proton exchange composite membranes.

    PubMed

    Salarizadeh, Parisa; Javanbakht, Mehran; Pourmahdian, Saeed; Bagheri, Ahmad; Beydaghi, Hossein; Enhessari, Morteza

    2016-06-15

    Modifying surfaces of nanoparticles with silane coupling agent provides a simple method to alter their surface properties and improve their dispersibility in organic solvents and polymer matrix. Fe2TiO5 nanoparticles (IT) were modified with 3-aminopropyltriethoxysilane (APTES) as novel reinforcing filler for proton exchange membranes. The main operating parameters such as reaction time (R.T), APTES/IT and triethylamine (TEA)/IT ratios have been optimized for maximum grafting efficiency. The optimum conditions for R.T, APTES/IT and TEA/IT ratios were 6h, 4 and 0.3 respectively. It was observed that the APTES/IT and TEA/IT ratios were the most significant parameters affecting the grafting percentage. Modified nanoparticles were characterized using FT-IR, TGA, SEM, TEM and XRD techniques. Effects of modified nanoparticles in proton exchange membrane fuel cells (PEMFC) were evaluated. The resulting nanocomposite membranes exhibited higher proton conductivity in comparison with pristine SPPEK and SPPEK/IT membranes. This increase is attributed to connectivity of the water channels which creates more direct pathways for proton transport. Composite membrane with 3% AIT (6.46% grafting amount) showed 0.024Scm(-1) proton conductivity at 25°C and 149mWcm(-2) power density (at 0.5V) at 80°C which were about 243% and 51%, respectively higher than that of pure SPPEK. PMID:27023633

  15. High resolution deuterium NMR studies of bacterial metabolism

    SciTech Connect

    Aguayo, J.B.; Gamcsik, M.P.; Dick, J.D.

    1988-12-25

    High resolution deuterium NMR spectra were obtained from suspensions of five bacterial strains: Escherichia coli, Clostridium perfringens, Klebsiella pneumoniae, Proteus mirabilis, and Staphylococcus aureus. Deuterium-labeled D-glucose at C-1, C-2, and C-6 was used to monitor dynamically anaerobic metabolism. The flux of glucose through the various bacterial metabolic pathways could be determined by following the disappearance of glucose and the appearance of the major end products in the 2H NMR spectrum. The presence of both labeled and unlabeled metabolites could be detected using 1H NMR spectroscopy since the proton resonances in the labeled species are shifted upfield due to an isotopic chemical shift effect. The 1H-1H scalar coupling observed in both the 2H and 1H NMR spectra was used to assign definitively the resonances of labeled species. An increase in the intensity of natural abundance deuterium signal of water can be used to monitor pathways in which a deuteron is lost from the labeled metabolite. The steps in which label loss can occur are outlined, and the influence these processes have on the ability of 2H NMR spectroscopy to monitor metabolism are assessed.

  16. Luminescence dynamics and {sup 13}C NMR characteristics of dinuclear complexes exhibiting coupled lanthanide(III) cation pairs

    SciTech Connect

    Matthews, K.D.; Bailey-Folkes, S.A.; Kahwa, I.A.

    1992-08-20

    Luminescence and cross-polarization magic angle spinning (CP-MAS) {sup 13}C NMR properties of lanthanide dinuclear macrocyclic complexes of a compartmental Schiff base chelate (1) derived from the condensation of 2,6-diformyl-p-cresol and 3,6-dioxa-1,8-octanediamine are reported. The Schiff base chromophore in 1 is a strong light absorber and an efficient sensitizer for intense Tb{sup 3+}({sup 5}D{sub 4}) and Eu{sup 3+}({sup 5}D{sub 0})(T < 110 K ) emission which does not exhibit self-quenching effects. Emission from Tb{sup 3+} is sensitized by the ligand singlet state; in striking contrast, Eu{sup 3+} emission is sensitized by the triplet state and reveals an unusual nonradiative quenching process at T > 110 K with a thermal barrier of {approx} 2300 cm{sup {minus}1}. Weak emission is observed from Dy{sup 3+}({sup 4}F{sub 9/2}), Sm{sup 3+}({sup 4}G{sub 5/2}), and Pr{sup 3+}({sup 1}D{sub 2}) diluted in Gd{sup 3+} (i.e., from Gd{sup 3+}-Ln{sup 3+} heteropairs, Ln = Pr, Sm, Dy). Intramolecular metal-metal (Ln-Ln = 4 {Angstrom}) interactions account for the greatly quenched emission from Sm{sup 3+}-Sm{sup 3+} and Dy{sup 3+}-Dy{sup 3+} homopairs compared to Gd{sup 3+}-Ln heteropairs (Ln = Sm, Dy). Gd{sup 3+}-Ln{sup 3+} emission lifetimes at 77 K are 1610 (Tb{sup 3+}), 890 (Eu{sup 3+}), 14 (Dy{sup 3+}) and {approx} 13 {mu}s (Sm{sup 3+}). Nonradiative relaxation processes at 77 K in dilute Ln{sup 3+}:Gd{sub 2}1(NO{sub 3}){sub 4}{center_dot}H{sub 2}O, being temperature independent for Sm{sup 3+} and Eu{sup 3+} but temperature dependent for Tb{sup 3+}, follow the energy gap law with {alpha} {approx} - 10{sup {minus}3} cm and B {approx} 2 x 10{sup 8} s{sup {minus}1}. CP-MAS data show paramagnetic broadening of {sup 13}C resonances which increases with the magnetic moment of Ln{sup 3+}. Surprisingly, no significant shifts in resonance positions corresponding to the changing nature of paramagnetic Ln{sup 3+} ions are observed. 43 refs., 8 figs., 2 tabs.

  17. Mechanism of dilute-spin-exchange in solid-state NMR

    SciTech Connect

    Lu, George J.; Opella, Stanley J.

    2014-03-28

    In the stationary, aligned samples used in oriented sample (OS) solid-state NMR, {sup 1}H-{sup 1}H homonuclear dipolar couplings are not attenuated as they are in magic angle spinning solid-state NMR; consequently, they are available for participation in dipolar coupling-based spin-exchange processes. Here we describe analytically the pathways of {sup 15}N-{sup 15}N spin-exchange mediated by {sup 1}H-{sup 1}H homonuclear dipolar couplings. The mixed-order proton-relay mechanism can be differentiated from the third spin assisted recoupling mechanism by setting the {sup 1}H to an off-resonance frequency so that it is at the “magic angle” during the spin-exchange interval in the experiment, since the “magic angle” irradiation nearly quenches the former but only slightly attenuates the latter. Experimental spectra from a single crystal of N-acetyl leucine confirm that this proton-relay mechanism plays the dominant role in {sup 15}N-{sup 15}N dilute-spin-exchange in OS solid-state NMR in crystalline samples. Remarkably, the “forbidden” spin-exchange condition under “magic angle” irradiation results in {sup 15}N-{sup 15}N cross-peaks intensities that are comparable to those observed with on-resonance irradiation in applications to proteins. The mechanism of the proton relay in dilute-spin-exchange is crucial for the design of polarization transfer experiments.

  18. NMR imaging microscopy

    SciTech Connect

    Not Available

    1986-10-01

    In the past several years, proton nuclear magnetic resonance (NMR) imaging has become an established technique in diagnostic medicine and biomedical research. Although much of the work in this field has been directed toward development of whole-body imagers, James Aguayo, Stephen Blackband, and Joseph Schoeninger of the Johns Hopkins University School of Medicine working with Markus Hintermann and Mark Mattingly of Bruker Medical Instruments, recently developed a small-bore NMR microscope with sufficient resolution to image a single African clawed toad cell (Nature 1986, 322, 190-91). This improved resolution should lead to increased use of NMR imaging for chemical, as well as biological or physiological, applications. The future of NMR microscopy, like that of many other newly emerging techniques, is ripe with possibilities. Because of its high cost, however, it is likely to remain primarily a research tool for some time. ''It's like having a camera,'' says Smith. ''You've got a way to look at things at very fine levels, and people are going to find lots of uses for it. But it is a very expensive technique - it costs $100,000 to add imaging capability once you have a high-resolution NMR, which itself is at least a $300,000 instrument. If it can answer even a few questions that can't be answered any other way, though, it may be well worth the cost.''

  19. Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-Molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein

    PubMed Central

    Cerminara, Michele; Campos, Luis A.; Ramanathan, Ravishankar; Muñoz, Victor

    2013-01-01

    A battery of thermodynamic, kinetic, and structural approaches has indicated that the small α-helical protein BBL folds-unfolds via the one-state downhill scenario. Yet, single-molecule fluorescence spectroscopy offers a more conflicting view. Single-molecule experiments at pH 6 show a unique half-unfolded conformational ensemble at mid denaturation, whereas other experiments performed at higher pH show a bimodal distribution, as expected for two-state folding. Here we use thermodynamic and laser T-jump kinetic experiments combined with theoretical modeling to investigate the pH dependence of BBL stability, folding kinetics and mechanism within the pH 6–11 range. We find that BBL unfolding is tightly coupled to the protonation of one of its residues with an apparent pKa of ∼7. Therefore, in chemical denaturation experiments around neutral pH BBL unfolds gradually, and also converts in binary fashion to the protonated species. Moreover, under the single-molecule experimental conditions (denaturant midpoint and 279 K), we observe that proton transfer is much slower than the ∼15 microseconds folding-unfolding kinetics of BBL. The relaxation kinetics is distinctly biphasic, and the overall relaxation time (i.e. 0.2–0.5 ms) becomes controlled by the proton transfer step. We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. Interestingly, this analysis suggests that BBL unfolds following a one-state downhill folding mechanism at all conditions. Accordingly, the source of the bimodal distributions observed during denaturation at pH 7–8 is the splitting of the unique conformational ensemble of BBL onto two slowly inter-converting protonation species. Both, the unprotonated and protonated species unfold gradually (one-state downhill), but they exhibit different degree of unfolding at any

  20. Roles of multiple-proton transfer pathways and proton-coupled electron transfer in the reactivity of the bis-FeIV state of MauG

    PubMed Central

    Ma, Zhongxin; Williamson, Heather R.; Davidson, Victor L.

    2015-01-01

    The high-valent state of the diheme enzyme MauG exhibits charge–resonance (CR) stabilization in which the major species is a bis-FeIV state with one heme present as FeIV=O and the other as FeIV with axial heme ligands provided by His and Tyr side chains. In the absence of its substrate, the high-valent state is relatively stable and returns to the diferric state over several minutes. It is shown that this process occurs in two phases. The first phase is redistribution of the resonance species that support the CR. The second phase is the loss of CR and reduction to the diferric state. Thermodynamic analysis revealed that the rates of the two phases exhibited different temperature dependencies and activation energies of 8.9 and 19.6 kcal/mol. The two phases exhibited kinetic solvent isotope effects of 2.5 and 2.3. Proton inventory plots of each reaction phase exhibited extreme curvature that could not be fit to models for one- or multiple-proton transfers in the transition state. Each did fit well to a model for two alternative pathways for proton transfer, each involving multiple protons. In each case the experimentally determined fractionation factors were consistent with one of the pathways involving tunneling. The percent of the reaction that involved the tunneling pathway differed for the two reaction phases. Using the crystal structure of MauG it was possible to propose proton–transfer pathways consistent with the experimental data using water molecules and amino acid side chains in the distal pocket of the high-spin heme. PMID:26283395

  1. Reaction dynamics and proton coupled electron transfer: studies of tyrosine-based charge transfer in natural and biomimetic systems.

    PubMed

    Barry, Bridgette A

    2015-01-01

    In bioenergetic reactions, electrons are transferred long distances via a hopping mechanism. In photosynthesis and DNA synthesis, the aromatic amino acid residue, tyrosine, functions as an intermediate that is transiently oxidized and reduced during long distance electron transfer. At physiological pH values, oxidation of tyrosine is associated with a deprotonation of the phenolic oxygen, giving rise to a proton coupled electron transfer (PCET) reaction. Tyrosine-based PCET reactions are important in photosystem II, which carries out the light-induced oxidation of water, and in ribonucleotide reductase, which reduces ribonucleotides to form deoxynucleotides. Photosystem II contains two redox-active tyrosines, YD (Y160 in the D2 polypeptide) and YZ (Y161 in the D1 polypeptide). YD forms a light-induced stable radical, while YZ functions as an essential charge relay, oxidizing the catalytic Mn₄CaO₅ cluster on each of four photo-oxidation reactions. In Escherichia coli class 1a RNR, the β2 subunit contains the radical initiator, Y122O•, which is reversibly reduced and oxidized in long range electron transfer with the α2 subunit. In the isolated E. coli β2 subunit, Y122O• is a stable radical, but Y122O• is activated for rapid PCET in an α2β2 substrate/effector complex. Recent results concerning the structure and function of YD, YZ, and Y122 are reviewed here. Comparison is made to recent results derived from bioengineered proteins and biomimetic compounds, in which tyrosine-based charge transfer mechanisms have been investigated. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems. PMID:25260243

  2. Role of the tryptophan residues in proton-coupled folate transporter (PCFT-SLC46A1) function.

    PubMed

    Najmi, Mitra; Zhao, Rongbao; Fiser, Andras; Goldman, I David

    2016-07-01

    The proton-coupled folate transporter (PCFT) mediates folate absorption across the brush-border membrane of the proximal small intestine and is required for folate transport across the choroid plexus into the cerebrospinal fluid. In this study, the functional role and accessibility of the seven PCFT Trp residues were assessed by the substituted-cysteine accessibility method. Six Trp residues at a lipid-aqueous interface tolerated Cys substitution in terms of protein stability and function. W85C, W202C, and W213C were accessible to N-biotinyl aminoethylmethanethiosulfonate; W48C and W299C were accessible only after treatment with dithiotreitol (DTT), consistent with modification of these residues by an endogenous thiol-reacting molecule and their extracellular location. Neither W107C nor W333C was accessible (even after DTT) consistent with their cytoplasmic orientation. Biotinylation was blocked by pemetrexed only for the W48C (after DTT), W85C, W202C residues. Function was impaired only for the W299C PCFT mutant located in the 4th external loop between the 7th and 8th transmembrane helices. Despite its aqueous location, function could only be fully preserved with Phe and, to a lesser extent, Ala substitutions. There was a 6.5-fold decrease in the pemetrexed influx Vmax and a 3.5- and 6-fold decrease in the influx Kt and Ki, respectively, for the W299S PCFT. The data indicate that the hydrophobicity of the W299 residue is important for function suggesting that during the transport cycle this residue interacts with the lipid membrane thereby impacting on the oscillation of the carrier and, indirectly, on the folate binding pocket. PMID:27251438

  3. Metabolic targeting of oncogene MYC by selective activation of the proton-coupled monocarboxylate family of transporters.

    PubMed

    Gan, L; Xiu, R; Ren, P; Yue, M; Su, H; Guo, G; Xiao, D; Yu, J; Jiang, H; Liu, H; Hu, G; Qing, G

    2016-06-01

    Deregulation of the MYC oncogene produces Myc protein that regulates multiple aspects of cancer cell metabolism, contributing to the acquisition of building blocks essential for cancer cell growth and proliferation. Therefore, disabling Myc function represents an attractive therapeutic option for cancer treatment. However, pharmacological strategies capable of directly targeting Myc remain elusive. Here, we identified that 3-bromopyruvate (3-BrPA), a drug candidate that primarily inhibits glycolysis, preferentially induced massive cell death in human cancer cells overexpressing the MYC oncogene, in vitro and in vivo, without appreciable effects on those exhibiting low MYC levels. Importantly, pharmacological inhibition of glutamine metabolism synergistically potentiated the synthetic lethal targeting of MYC by 3-BrPA due in part to the metabolic disturbance caused by this combination. Mechanistically, we identified that the proton-coupled monocarboxylate transporter 1 (MCT1) and MCT2, which enable efficient 3-BrPA uptake by cancer cells, were selectively activated by Myc. Two regulatory mechanisms were involved: first, Myc directly activated MCT1 and MCT2 transcription by binding to specific recognition sites of both genes; second, Myc transcriptionally repressed miR29a and miR29c, resulting in enhanced expression of their target protein MCT1. Of note, expressions of MCT1 and MCT2 were each significantly elevated in MYCN-amplified neuroblastomas and C-MYC-overexpressing lymphomas than in tumors without MYC overexpression, correlating with poor prognosis and unfavorable patient survival. These results identify a novel mechanism by which Myc sensitizes cells to metabolic inhibitors and validate 3-BrPA as potential Myc-selective cancer therapeutics. PMID:26434591

  4. Reversible proton transfer phenomenon in the 2,4-dichlorophenol-triethylamine hydrogen-bonded complex studied by low-temperature 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Ilczyszyn, Marek; Ratajczak, Henryk; Ladd, John A.

    1988-12-01

    Low-temperature 1H NMR studies of the bridging OHN signal in the hydrogen-bonded complex formed between 2,4-dichlorophenol and triethylamine in C 2H 5Cl solution have demonstrated for the first time that separate signals for the molecular and ion-pair forms of this type of system can be observed. The temperature dependence of these signals leads to thermodynamic and kinetic quantities which suggest that the potential energy profile of the hydrogen bond is roughly symmetric with a double minimum.

  5. HC[triple bond]P and H3C-C[triple bond]P as proton acceptors in protonated complexes containing two phosphorus bases: structures, binding energies, and spin-spin coupling constants.

    PubMed

    Alkorta, Ibon; Elguero, José; Bene, Janet E Del

    2007-10-01

    Ab initio calculations at the MP2/aug'-cc-pVTZ level have been carried out to investigate the structures and binding energies of cationic complexes involving protonated sp, sp2, and sp3 phosphorus bases as proton donor ions and the sp-hybridized phosphorus bases H-C[triple bond]P and H3C-C[triple bond]P as proton acceptors. These proton-bound complexes exhibit a variety of structural motifs, but all are stabilized by interactions that occur through the pi cloud of the acceptor base. The binding energies of these complexes range from 6 to 15 kcal/mol. Corresponding complexes with H3C-C[triple bond]P as the proton acceptor are more stable than those with H-C[triple bond]P as the acceptor, a reflection of the greater basicity of H3C-C[triple bond]P. In most complexes with sp2- or sp3-hybridized P-H donor ions, the P-H bond lengthens and the P-H stretching frequency is red-shifted relative to the corresponding monomers. Complex formation also leads to a lengthening of the C[triple bond]P bond and a red shift of the C[triple bond]P stretching vibration. The two-bond coupling constants 2pihJ(P-P) and 2pihJ(P-C) are significantly smaller than 2hJ(P-P) and 2hJ(P-C) for complexes in which hydrogen bonding occurs through lone pairs of electrons on P or C. This reflects the absence of significant s electron density in the hydrogen-bonding regions of these pi complexes. PMID:17760429

  6. Large NMR signals and polarization asymmetries.

    SciTech Connect

    Penttila, S. I.

    1998-11-25

    A large modulation in the series Q-meter can lead to nonlinear NMR signals and asymmetric polarization values. With a careful circuit analysis the nonlinearity can be estimated and corrections to polarization can be determined as a function of the strength of the modulation. We describe the recent LAMPF polarized proton target experiment, its NMR measurement and corrections to the measured polarizations.

  7. A Novel High-Resolution and Sensitivity-Enhanced Three-Dimensional Solid-State NMR Experiment Under Ultrafast Magic Angle Spinning Conditions.

    PubMed

    Zhang, Rongchun; Pandey, Manoj Kumar; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

    2015-01-01

    Although magic angle spinning (MAS) solid-state NMR is a powerful technique to obtain atomic-resolution insights into the structure and dynamics of a variety of chemical and biological solids, poor sensitivity has severely limited its applications. In this study, we demonstrate an approach that suitably combines proton-detection, ultrafast-MAS and multiple frequency dimensions to overcome this limitation. With the utilization of proton-proton dipolar recoupling and double quantum (DQ) coherence excitation/reconversion radio-frequency pulses, very high-resolution proton-based 3D NMR spectra that correlate single-quantum (SQ), DQ and SQ coherences of biological solids have been obtained successfully for the first time. The proposed technique requires a very small amount of sample and does not need multiple radio-frequency (RF) channels. It also reveals information about the proximity between a spin and a certain other dipolar-coupled pair of spins in addition to regular SQ/DQ and SQ/SQ correlations. Although (1)H spectral resolution is still limited for densely proton-coupled systems, the 3D technique is valuable to study dilute proton systems, such as zeolites, small molecules, or deuterated samples. We also believe that this new methodology will aid in the design of a plethora of multidimensional NMR techniques and enable high-throughput investigation of an exciting class of solids at atomic-level resolution. PMID:26138791

  8. Isolating Friedelin from Cork and Reducing It to Friedelinol and Epifriedelinol. A Project Involving NMR Spectrometry and Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Lefevre, Joseph W.; McNeill, Kristin I.; Moore, Janet L.

    2001-04-01

    In this four-week project, the pentacyclic triterpene friedelin is isolated from laboratory cork. The ground cork is refluxed in ethyl acetate, from which crude friedelin crystallizes. The crude product is analyzed by thin-layer chromatography and purified by flash chromatography. The resulting pure friedelin is reduced to friedelinol and epifriedelinol using different reduction conditions. Each product is analyzed by 1H NMR spectrometry and identified by comparing the CHOH signal with the corresponding signal in the model compounds, menthol and neomenthol. Finally, from computer-generated 3-D molecular models of each alcohol, key dihedral angles are measured and used to calculate three proton-proton coupling constants (J values) involving the CHOH proton. These values are compared to the actual J values determined by NMR spectrometry.

  9. Change of translational-rotational coupling in liquids revealed by field-cycling {sup 1}H NMR

    SciTech Connect

    Meier, R.; Schneider, E.; Rössler, E. A.

    2015-01-21

    Applying the field-cycling nuclear magnetic resonance technique, the frequency dependence of the {sup 1}H spin-lattice relaxation rate, R{sub 1}(ω)=T{sub 1}{sup −1}(ω), is measured for propylene glycol (PG) which is increasingly diluted with deuterated chloroform. A frequency range of 10 kHz–20 MHz and a broad temperature interval from 220 to about 100 K are covered. The results are compared to those of experiments, where glycerol and o-terphenyl are diluted with their deuterated counter-part. Reflecting intra- as well as intermolecular relaxation, the dispersion curves R{sub 1}(ω,x) (x denotes mole fraction PG) allow to extract the rotational time constant τ{sub rot}(T, x) and the self-diffusion coefficient D(T, x) in a single experiment. The Stokes-Einstein-Debye (SED) relation is tested in terms of the quantity D(T, x) τ{sub rot}(T, x) which provides a measure of an effective hydrodynamic radius or equivalently of the spectral separation of the translational and the rotational relaxation contribution. In contrast to o-terphenyl, glycerol and PG show a spectral separation much larger than suggested by the SED relation. In the case of PG/chloroform mixtures, not only an acceleration of the PG dynamics is observed with increasing dilution but also the spectral separation of rotational and translational relaxation contributions continuously decreases. Finally, following a behavior similar to that of o-terphenyl already at about x = 0.6; i.e., while D(T, x) τ{sub rot}(T, x) in the mixture is essentially temperature independent, it strongly increases with x signaling thus a change of translational-rotational coupling. This directly reflects the dissolution of the hydrogen-bond network and thus a change of solution structure.

  10. High field and 2D-nmr studies with the aporphine alkaloid glaucine.

    PubMed

    Kerr, K M; Kook, A M; Davis, P J

    1986-01-01

    The aporphine alkaloid glaucine (1) was examined by comparison of the high field (600 MHz) 1H-nmr spectra of 1 vs. racemic 6a,7,7-trideutereoglaucine (4,5), by computer-simulated 1H-nmr spectra at 600 MHz, by using decoupled proton spectra, and two-dimensional COSY and HETCOR experiments with 1 at 500 and 360 MHz, respectively, and using high field (90 MHZ) 13C-nmr of S-(+)-glaucine (1). Emphasis was placed on the resolution of the chemical shifts and coupling constants for the H-4 alpha, H-4 beta, H-5 alpha, H-5 beta, H-6 alpha, H-7 alpha, and H-7 beta alicyclic protons of the molecule, which were previously unassigned. The complete assignment of the alicyclic protons of 1 by 1H-nmr was required for the structural elucidation of deuterated analogs of glaucine, which will be used in microbial transformation studies to determine the stereochemical course of aporphine dehydrogenation by the fungi Fusarium solani (ATCC 12823) and Aspergillus flavipes (ATCC 1030). PMID:3783155

  11. Direct (13)C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA.

    PubMed

    Fürtig, Boris; Schnieders, Robbin; Richter, Christian; Zetzsche, Heidi; Keyhani, Sara; Helmling, Christina; Kovacs, Helena; Schwalbe, Harald

    2016-03-01

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond (1)H detection. Here, we develop (13)C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for (13)C direct detection allows correlations of donor-acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed (13)C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics. PMID:26852414

  12. Chromatographic NMR in NMR solvents

    NASA Astrophysics Data System (ADS)

    Carrara, Caroline; Viel, Stéphane; Delaurent, Corinne; Ziarelli, Fabio; Excoffier, Grégory; Caldarelli, Stefano

    2008-10-01

    Recently, it was demonstrated that pseudo-chromatographic NMR experiments could be performed using typical chromatographic solids and solvents. This first setup yielded improved separation of the spectral components of the NMR spectra of mixtures using PFG self-diffusion measurements. The method (dubbed Chromatographic NMR) was successively shown to possess, in favorable cases, superior resolving power on non-functionalized silica, compared to its LC counterpart. To further investigate the applicability of the method, we studied here the feasibility of Chromatographic NMR in common deuterated solvents. Two examples are provided, using deuterated chloroform and water, for homologous compounds soluble in these solvents, namely aromatic molecules and alcohols, respectively.

  13. Petrophysical applications of NMR imaging

    SciTech Connect

    Rothwell, W.P.; Vinegar, H.J.

    1985-12-01

    A system for obtaining high-resolution NMR images of oil field cores is described. Separate proton density and T/sub 2/ relaxation images are obtained to distinguish spatial variations of fluid-filled porosity and the physical nature of the pores. Results are presented for typical sandstones.

  14. Spectroscopic separation of (13) C NMR spectra of complex isomeric mixtures by the CSSF-TOCSY-INEPT experiment.

    PubMed

    Yang, Lu; Moreno, Aitor; Fieber, Wolfgang; Brauchli, Robert; Sommer, Horst

    2015-04-01

    Isomeric mixtures from synthetic or natural origins can pose fundamental challenges for their chromatographic separation and spectroscopic identification. A novel 1D selective NMR experiment, chemical shift selective filter (CSSF)-TOCSY-INEPT, is presented that allows the extraction of (13) C NMR subspectra of discrete isomers in complex mixtures without physical separation. This is achieved via CSS excitation of proton signals in the (1) H NMR mixture spectrum, propagation of the selectivity by polarization transfer within coupled (1) H spins, and subsequent relaying of the magnetization from (1) H to (13) C by direct INEPT transfer to generate (13) C NMR subspectra. Simple consolidation of the subspectra yields (13) C NMR spectra for individual isomers. Alternatively, CSSF-INEPT with heteronuclear long-range transfer can correlate the isolated networks of coupled spins and therefore facilitate the reconstruction of the (13) C NMR spectra for isomers containing multiple spin systems. A proof-of-principle validation of the CSSF-TOCSY-INEPT experiment is demonstrated on three mixtures with different spectral and structural complexities. The results show that CSSF-TOCSY-INEPT is a versatile, powerful tool for deconvoluting isomeric mixtures within the NMR tube with unprecedented resolution and offers unique, unambiguous spectral information for structure elucidation. PMID:25616134

  15. Deuteron and proton NMR study of D2, p-dichlorobenzene and 1,3,5-trichlorobenzene in bimesogenic liquid crystals with two nematic phases

    NASA Astrophysics Data System (ADS)

    Burnell, E. E.; Ahmed, Z.; Welch, C.; Mehl, G. H.; Dong, R. Y.

    2016-08-01

    The solutes dideuterium, 1,3,5-trichlorobenzene and p-dichlorobenzene (pdcb) are co-dissolved in a 61/39 wt% mixture of CBC9CB/5CB, a bimesogenic liquid crystal with two nematic phases. NMR spectra are collected for each solute. The local electric field gradient (FZZ) is obtained from the dideuterium spectrum. A double Maier-Saupe potential (MSMS) is used to rationalize the order parameters of pdcb. The liquid-crystal fields G1 and G2 are taken to be due to size and shape interactions and interactions between the solute molecular quadrupole and the mean FZZ of the medium. The FZZ 's obtained from D2 and G2 (from pdcb) are compared and discussed.

  16. Nuclear magnetic resonance studies of phosphorus(v) pesticides. Part I. Chemical shifts of protons as a means of identification of pesticides

    USGS Publications Warehouse

    Babad, H.; Herbert, W.; Goldberg, M.C.

    1968-01-01

    Correlations of structural and proton chemical-hift data for 40 commercial phosphorus(V) pesticides are reported. Correlations of structure with the phosphorus coupling constants are discussed, and general trends are noted which aid in the use of NMR as a tool for identification and analysis of phosphorus(V) compounds. ?? 1968.

  17. Quantitation of metabolic compartmentation in hyperammonemic brain by natural abundance 13C-NMR detection of 13C-15N coupling patterns and isotopic shifts.

    PubMed

    Lapidot, A; Gopher, A

    1997-02-01

    In the present study, the removal of cerebral ammonia by glutamine synthetase (GS) and by reductive amination of 2-oxoglutarate by glutamate dehydrogenase in the presence of an amino donor group, was determined in hyperammonemic rabbit brains. The 15N enrichments of brain metabolite alpha-amino and amide positions of glutamine, glutamate, and alanine were determined by the indirect detection of 15N-labeled compounds of the 13C-15N spin coupling patterns of natural abundance 13C-NMR spectra. The 13C-NMR spectra of brain extracts were obtained from rabbits infused with 15NH4Cl with or without intraperitoneal infusion of the GS inhibitor, L-methionine DL-sulfoximine, in a reasonable acquisition time period. When 15NH4Cl was infused, [5-15N]glutamine and [2-15N]glutamine concentrations reached 5.2 mumol/100 mg protein and 3.6 mumol/100 mg protein, respectively, which indicates the relatively high activity of reductive amination of 2-oxoglutarate in the glutamate dehydrogenase reaction. The low concentration of [2-15N]glutamate, which is about 30% of that of [2-15N]glutamine obtained in this study, suggests that very little glutamine serves as a precursor of neuronal glutamate. When GS was inhibited by L-methionine DL-sulfoximine, a flux of 15NH4+ via the residual activity of GS was accompanied by an apparent increase of [2-15N]glutamate and [15N]alanine concentrations (2.9 mumol/100 mg protein and 1.8 mumol/100 mg protein, respectively). These findings and those obtained from 13C-13C isotopomer analysis (Lapidot and Gopher, 1994b) suggest that astrocytic 2-oxoglutarate is partially utilized (together with an amino group donor) as a precursor for neuronal glutamate in the hyperammonemic brain when GS is inhibited. This process can partly replace GS activity in metabolizing ammonia in the hyperammonemic rabbit brain. PMID:9057821

  18. First high-power model of the annular-ring coupled structure for use in the Japan Proton Accelerator Research Complex linac

    NASA Astrophysics Data System (ADS)

    Ao, Hiroyuki; Yamazaki, Yoshishige

    2012-01-01

    A prototype cavity for the annular-ring coupled structure (ACS) for use in the Japan Proton Accelerator Research Complex (J-PARC) linac has been developed to confirm the feasibility of achieving the required performance. This prototype cavity is a buncher module, which includes ten accelerating cells in total. The ACS cavity is formed by the silver brazing of ACS half-cell pieces stacked in a vacuum furnace. The accelerating cell of the ACS is surrounded by a coupling cell. We, therefore, tuned the frequencies of the accelerating and coupling cells by an ultraprecision lathe before brazing, taking into account the frequency shift due to brazing. The prototype buncher module was successfully conditioned up to 600 kW, which corresponds to an accelerating field that is higher than the designed field of 4.1MV/m by 30%. We describe the frequency-tuning results for the prototype buncher module and its high-power conditioning.

  19. The Proton-Sensing G-Protein Coupled Receptor GPR4 Promotes Angiogenesis in Head and Neck Cancer

    PubMed Central

    Chen, Xiaohong; Zhong, Qi; Huang, Junwei; Zhang, Yang; Guo, Wei; Yang, Zheng; Ding, Shuo; Chen, Ping

    2016-01-01

    Squamous cell carcinoma of the head and neck (SCCHN) is an aggressive disease with poor survival and is the sixth most common cancer worldwide. Gastroesophageal reflux is a common event in SCCHN patients. GPR4 is a proton-sensing G-protein coupled receptor, which can be activated by acidosis. The objective of this study was to explore the role of GPR4 in acid exposure and tumor angiogenesis in SCCHN. In this study, we confirmed that overexpressing GPR4 in SCCHN cells could increase the expression and secretion of IL6, IL8 and VEGFA at pH 5.9. This effect could be inhibited by SB203580 (a p38 inhibitor). Western blot analysis indicated that phosphorylation of p38 increased in GPR4 infected cells at pH 5.9, which could be inhibited by SB203580. In tube formation assay, HMEC-1 cells were incubated with conditioned medium (CM, pH 5.9, 6.5, 7.4) derived from control and GPR4 infected SCCHN cells. Tube length was significantly increased in HMEC-1 cells incubated with CM from GPR4 infected cells compared with control cells at pH5.9, which indicated the pro-angiogenic effect of GPR4 in acidic pH. The neutralizing antibodies of IL6, IL8 and VEGFA could inhibit tube formation of HMEC-1 cells. In vivo, the effect of GPR4 on angiogenesis was investigated with the chick chorioallantoic membrane (CAM) model. Control and GPR4 infected SCCHN cells were seeded onto the upper CAM surface (n = 5 in each group) and 5 μL DMEM/F12 (pH 5.9, 6.5, 7.4) was added to the surface of the cell every 24 h. Four days later, the upper CAM were harvested and the ratio of the vascular area to the CAM area was quantified using Image-Pro Plus 6.0 software. GPR4 infected cells could recruit more vascular than control cells at pH5.9. In conclusion, we suggested that GPR4 induces angiogenesis via GPR4-induced p38-mediated IL6, IL8 and VEGFA secretion at acidic extracellular pH in SCCHN. PMID:27078157

  20. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1992-05-27

    This report covers the progress made on the title project for the project period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups that determine the reactivity of coals. Special attention is being paid to methods that are compatible with the very high magic angle sample spinning rates needed for operation at the high magnetic field strengths available today. Polarization inversion methods utilizing the difference in heat capacities of small groups of spins are particularly promising. Methods combining proton-proton spin diffusion with {sup 13}C CPMAS readout are being developed to determine the connectivity of functional groups in coals in a high sensitivity relay type of experiment. Additional work is aimed a delineating the role of methyl group rotation in the proton NMR relaxation behavior of coals.

  1. Communication: Molecular dynamics and {sup 1}H NMR of n-hexane in liquid crystals

    SciTech Connect

    Weber, Adrian C. J.; Burnell, E. Elliott; Meerts, W. Leo; Lange, Cornelis A. de; Dong, Ronald Y.; Muccioli, Luca Pizzirusso, Antonio Zannoni, Claudio

    2015-07-07

    The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.

  2. NMR studies of molecules in liquid crystals and graphite

    SciTech Connect

    Rosen, M.E.

    1992-06-01

    NMR experiments to measure proton dipole couplings were performed on a series of n-alkanes (n-hexane through n-decane) dissolved in nematic liquid crystals. Computer modeling of the experimental NMR-spectra was done using several different models for intermolecular interactions in these systems. The model of Photinos et al. was found to be best in describing the intermolecular interactions in these systems and can provide a statistical picture of the conformation and orientation of the alkane molecules in their partially-oriented environment. Order parameters and conformational distributions for the alkanes can be calculated from the modeling. The alkanes are found to have conformational distributions very much like those found in liquid alkanes. Proton NMR spectra of tetrahydrofuran (THF) intercalated in two graphite intercalation compounds were also measured. Computer simulations of these spectra provide a picture of THF in the constrained environment between the graphene layers where the THF is oriented at a particular angle, can translate and rotate freely, but does not appear to pseudorotate.

  3. Structural studies by proton-NMR spectroscopy of plant horseradish peroxidase C, the wild-type recombinant protein from Escherichia coli and two protein variants, Phe41----Val and Arg38----Lys.

    PubMed

    Veitch, N C; Williams, R J; Bray, R C; Burke, J F; Sanders, S A; Thorneley, R N; Smith, A T

    1992-07-15

    Wild-type recombinant horseradish peroxidase isoenzyme C and two protein variants, Phe41----Val and Arg38----Lys, have been characterised using both one- and two-dimensional NMR spectroscopy. Proton NMR spectra recorded in both resting and cyanide-ligated states of the proteins were compared with those of the corresponding plant peroxidase. The latter contains 18% carbohydrate in eight N-linked oligosaccharide side chains whereas the recombinant proteins are expressed in nonglycosylated form. The spectra of the plant enzyme and refolded recombinant protein are essentially identical with the exception of carbohydrate-linked resonances in the former, indicating that their solution structures are highly similar. This comparison also identifies classes of carbohydrate resonances in the plant enzyme which provides new information on the local environment and mobility of the oligosaccharide side chains. Comparison of the spectra of the cyanide-ligated states of the two variants and those of plant horseradish peroxidase C indicated that there were significant differences with respect to haem and haem-linked resonances. These could not be rationalised simply on the basis of the local perturbation expected from a single-site substitution. The two substitutions made to residues on the distal side of the haem apparently influenced the degree of imidazolate character of the proximal His170 imidazole ring thus perturbing the magnetic environment of the haem group. Inspection of the spectra of the Phe41----Val variant also showed that the resonances of a phenylalanine residue in the haem pocket had been incorrectly assigned to Phe41 in a previous study. A new assignment, based on additional information from two-dimensional nuclear Overhauser enhancement spectroscopy, was made to Phe152. The assignments made for the Phe41----Val variant were also used as a basis to investigate the structure of the complex formed with the aromatic donor molecule, benzhydroxamic acid. PMID:1633807

  4. Asymmetric protonation of EmrE

    PubMed Central

    Morrison, Emma A.; Robinson, Anne E.; Liu, Yongjia

    2015-01-01

    The small multidrug resistance transporter EmrE is a homodimer that uses energy provided by the proton motive force to drive the efflux of drug substrates. The pKa values of its “active-site” residues—glutamate 14 (Glu14) from each subunit—must be poised around physiological pH values to efficiently couple proton import to drug export in vivo. To assess the protonation of EmrE, pH titrations were conducted with 1H-15N TROSY-HSQC nuclear magnetic resonance (NMR) spectra. Analysis of these spectra indicates that the Glu14 residues have asymmetric pKa values of 7.0 ± 0.1 and 8.2 ± 0.3 at 45°C and 6.8 ± 0.1 and 8.5 ± 0.2 at 25°C. These pKa values are substantially increased compared with typical pKa values for solvent-exposed glutamates but are within the range of published Glu14 pKa values inferred from the pH dependence of substrate binding and transport assays. The active-site mutant, E14D-EmrE, has pKa values below the physiological pH range, consistent with its impaired transport activity. The NMR spectra demonstrate that the protonation states of the active-site Glu14 residues determine both the global structure and the rate of conformational exchange between inward- and outward-facing EmrE. Thus, the pKa values of the asymmetric active-site Glu14 residues are key for proper coupling of proton import to multidrug efflux. However, the results raise new questions regarding the coupling mechanism because they show that EmrE exists in a mixture of protonation states near neutral pH and can interconvert between inward- and outward-facing forms in multiple different protonation states. PMID:26573622

  5. Photo-induced water oxidation at the aqueous GaN (101¯0) interface: Deprotonation kinetics of the first proton-coupled electron-transfer step

    DOE PAGESBeta

    Ertem, Mehmed Z.; Kharche, Neerav; Batista, Victor S.; Hybertsen, Mark S.; Tully, John C.; Muckerman, James T.

    2015-03-12

    Photoeclectrochemical water splitting plays a key role in a promising path to the carbon-neutral generation of solar fuels. Wurzite GaN and its alloys (e.g., GaN/ZnO and InGaN) are demonstrated photocatalysts for water oxidation, and they can drive the overall water splitting reaction when coupled with co-catalysts for proton reduction. In the present work, we investigate the water oxidation mechanism on the prototypical GaN (101¯0) surface using a combined ab initio molecular dynamics and molecular cluster model approach taking into account the role of water dissociation and hydrogen bonding within the first solvation shell of the hydroxylated surface. The investigation ofmore » free-energy changes for the four proton-coupled electron-transfer (PCET) steps of the water oxidation mechanism shows that the first PCET step for the conversion of –Ga-OH to –Ga-O˙⁻ requires the highest energy input. We further examine the sequential PCETs, with the proton transfer (PT) following the electron transfer (ET), and find that photo-generated holes localize on surface –NH sites is thermodynamically more favorable than –OH sites. However, proton transfer from –OH sites with subsequent localization of holes on oxygen atoms is kinetically favored owing to hydrogen bonding interactions at the GaN (101¯0)–water interface. We find that the deprotonation of surface –OH sites is the limiting factor for the generation of reactive oxyl radical ion intermediates and consequently for water oxidation.« less

  6. Photo-induced water oxidation at the aqueous GaN (101¯0) interface: Deprotonation kinetics of the first proton-coupled electron-transfer step

    SciTech Connect

    Ertem, Mehmed Z.; Kharche, Neerav; Batista, Victor S.; Hybertsen, Mark S.; Tully, John C.; Muckerman, James T.

    2015-03-12

    Photoeclectrochemical water splitting plays a key role in a promising path to the carbon-neutral generation of solar fuels. Wurzite GaN and its alloys (e.g., GaN/ZnO and InGaN) are demonstrated photocatalysts for water oxidation, and they can drive the overall water splitting reaction when coupled with co-catalysts for proton reduction. In the present work, we investigate the water oxidation mechanism on the prototypical GaN (101¯0) surface using a combined ab initio molecular dynamics and molecular cluster model approach taking into account the role of water dissociation and hydrogen bonding within the first solvation shell of the hydroxylated surface. The investigation of free-energy changes for the four proton-coupled electron-transfer (PCET) steps of the water oxidation mechanism shows that the first PCET step for the conversion of –Ga-OH to –Ga-O˙⁻ requires the highest energy input. We further examine the sequential PCETs, with the proton transfer (PT) following the electron transfer (ET), and find that photo-generated holes localize on surface –NH sites is thermodynamically more favorable than –OH sites. However, proton transfer from –OH sites with subsequent localization of holes on oxygen atoms is kinetically favored owing to hydrogen bonding interactions at the GaN (101¯0)–water interface. We find that the deprotonation of surface –OH sites is the limiting factor for the generation of reactive oxyl radical ion intermediates and consequently for water oxidation.

  7. Fluorine detected 2D NMR experiments for the practical determination of size and sign of homonuclear F-F and heteronuclear C-F multiple bond J-coupling constants in multiple fluorinated compounds

    NASA Astrophysics Data System (ADS)

    Aspers, Ruud L. E. G.; Ampt, Kirsten A. M.; Dvortsak, Peter; Jaeger, Martin; Wijmenga, Sybren S.

    2013-06-01

    The use of fluorine in molecules obtained from chemical synthesis has become increasingly important within the pharmaceutical and agricultural industry. NMR characterization of these compounds is of great value with respect to their structure elucidation, their screening in metabolomics investigations and binding studies. The favorable NMR properties of the fluorine nucleus make NMR with fluorine detection of great value in this respect. A suite of NMR 2D F-F- and F-C-correlation experiments with fluorine detection was applied to the assignment of resonances, nJCF- and nJFF-couplings as well as the determination of their size and sign. The utilization of this experiment suite was exemplarily demonstrated for a highly fluorinated vinyl alkyl ether. Especially F-C HSQC and J-scaled F-C HMBC experiments allowed determining the size of the J-couplings of this compound. The relative sign of its homo- and heteronuclear couplings was achieved by different combinations of 2D NMR experiments, including non-selective and F2-selective F-C XLOC, F2-selective F-C HMQC, and F-F COSY. The F2-one/two-site selective F-C XLOC versions were found highly useful, as they led to simplifications of the common E.COSY patterns and resulted in a higher confidence level of the assignment by using selective excitation. The combination of F2-one/two-site selective F-C XLOC experiments with a F2-one-site selective F-C HMQC experiment provided the signs of all nJCF- and nJFF-couplings in the vinyl moiety of the test compound. Other combinations of experiments were found useful as well for special purposes when focusing for example on homonuclear couplings a combination of F-F COSY-10 with a F2-one-site selective F-C HMQC could be used. The E.COSY patterns in the spectra demonstrated were analyzed by use of the spin-selective displacement vectors, and in case of the XLOC also by use of the DQ- and ZQ-displacement vectors. The variety of experiments presented shall contribute to facilitate the

  8. Measurements of the Z Z production cross sections in the 2l 2ν channel in proton-proton collisions at √{s} = 7 and 8 TeV and combined constraints on triple gauge couplings

    NASA Astrophysics Data System (ADS)

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Lauwers, J.; Luyckx, S.; Ochesanu, S.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Randle-conde, A.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Zenoni, F.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Júnior, W. L. Aldá; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Martins, T. Dos Reis; Mora Herrera, C.; Pol, M. E.; Rebello Teles, P.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Hadjiiska, R.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Cheng, T.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Tao, J.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Zou, W.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Ellithi Kamel, A.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Skovpen, K.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Bernet, C.; Boudoul, G.; Bouvier, E.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Heister, A.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Preuten, M.; Raupach, F.; Sammet, J.; Schael, S.; Schulte, J. F.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Reithler, H.; Schmitz, S. 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J.; Lee, S.; Oh, Y. D.; Park, H.; Sakharov, A.; Son, D. C.; Kim, T. J.; Ryn, M. S.; Kim, J. Y.; Moon, D. H.; Song, S.; Choi, S.; Gyun, D.; Hong, B.; Jo, M.; Kim, H.; Kim, Y.; Lee, B.; Lee, K. S.; Park, S. K.; Roh, Y.; Yoo, H. D.; Choi, M.; Kim, J. H.; Park, I. C.; Ryu, G.; Choi, Y.; Choi, Y. K.; Goh, J.; Kim, D.; Kwon, E.; Lee, J.; Yu, I.; Juodagalvis, A.; Komaragiri, J. R.; Md Ali, M. A. B.; Wan Abdullah, W. A. T.; Casimiro Linares, E.; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-de La Cruz, I.; Hernandez-Almada, A.; Lopez-Fernandez, R.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Vazquez Valencia, F.; Pedraza, I.; Salazar Ibarguen, H. A.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Reucroft, S.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khan, W. 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F.; Missiroli, M.; Moran, D.; Brun, H.; Cuevas, J.; Fernandez Menendez, J.; Folgueras, S.; Gonzalez Caballero, I.; Brochero Cifuentes, J. A.; Cabrillo, I. J.; Calderon, A.; Duarte Campderros, J.; Fernandez, M.; Gomez, G.; Graziano, A.; Lopez Virto, A.; Marco, J.; Marco, R.; Martinez Rivero, C.; Matorras, F.; Munoz Sanchez, F. J.; Piedra Gomez, J.; Rodrigo, T.; Rodríguez-Marrero, A. Y.; Ruiz-Jimeno, A.; Scodellaro, L.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Benaglia, A.; Bendavid, J.; Benhabib, L.; Benitez, J. 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